Cannabis Annual Regulatory Fees 2026: The 30 September Deadline and the Medical Exemption Declaration

For Canadian cannabis licence holders, 30 September is one of the least forgiving dates on the regulatory calendar. By that day you must pay your annual regulatory fee invoice for the current fiscal year, and, if you sell only for medical purposes, submit the declaration that claims your exemption from that fee. Miss the exemption declaration for any reason and Health Canada must refuse it. There is no appeal, and the refusal converts your fee from the exemption basis to the full revenue-percentage basis.

This is a deadline explainer, not a report of a new law. The Health Canada cost recovery framework has not changed since 2025, but the 30 September deadline arrives every year and still catches licence holders out. This article sets out the verified fee figures, how the fee is calculated, exactly how the medical exemption works, and a practical filing checklist for cannabis and hemp licence holders.

Executive summary

In short: every cannabis licence holder pays an annual regulatory fee for each fiscal year they hold a valid licence, even for a single day. The fee is the higher of a minimum for your licence class or a percentage of your cannabis revenue. Sale for medical purposes licence holders can claim an exemption, but only by filing a declaration through the Cannabis tracking and licensing system (CTLS) by 30 September. Late declarations must be refused.

The annual regulatory fee invoice is due before 30 September of each fiscal year.
The medical-sale exemption declaration is also due by 30 September, or within 60 days of initial licensing for new holders.
The minimum fee is $2,500 for micro and nursery classes and $23,000 for standard classes.
The percentage is 1 per cent up to $1 million and 2.3 per cent above, for micro and nursery, and 2.3 per cent for standard classes.
If you miss the exemption deadline for any reason, Health Canada must refuse your request. Retain the underlying records regardless.

Obligation	Deadline	Where
Entry year fee (minimum for your class)	Within 60 days of your licence date	Invoice by email
Statement of cannabis revenue	Before 30 April	CTLS
Annual regulatory fee invoice	Before 30 September	Invoice by email
Medical exemption declaration	Before 30 September (or 60 days of licensing)	CTLS or email
Monthly sales data	By the 10th of each month	CTLS

What is the cannabis annual regulatory fee?

The cannabis annual regulatory fee is a cost recovery charge that every licence holder pays for each fiscal year they hold a valid licence. The federal fiscal year runs from 1 April to 31 March. You owe the fee even if your licence was valid for only one day in the year, and the amount is not reduced for a partial year, a suspension or a revocation. The fee is invoiced per site, so a site with several licences pays one minimum fee, at the higher applicable rate.

Your fee is the higher of two numbers: the minimum fee for your licence class, or a percentage of the cannabis revenue on your previous year's Statement of cannabis revenue. Cannabis revenue is the revenue from the sale of cannabis minus the amount you paid for cannabis, and it is treated as zero if that figure is negative. Taxes such as excise duty and GST or HST are excluded, as is revenue from transport, storage, distribution, processing or packaging services and from royalties, patents or leasing rights.

Licence class	Minimum fee	Percentage of cannabis revenue
Micro-cultivation, micro-processing, nursery	$2,500	1% up to $1M, 2.3% above $1M
Standard cultivation, standard processing, sale for medical purposes	$23,000	2.3%

One nuance saves money for combined sites. If a sale for medical purposes licence is combined with a micro-cultivation, micro-processing or nursery licence at the same site, you pay the lower rate rather than the standard rate. This annual regulatory fee is separate from the transactional fees you pay for specific licence actions, which we cover in our guide to cannabis sales licence costs and timelines.

The 30 September medical exemption declaration

The medical exemption lets a sale for medical purposes licence holder avoid the annual regulatory fee if it sells cannabis only within Canada to registered clients, a named responsible adult, or a person granted an exemption under section 140 of the Cannabis Act. To claim it you must file a declaration through CTLS, or by email, before 30 September of the fiscal year you are claiming, or within 60 days of initial licensing. This is not automatic. It must be filed every single year.

The hard edge is the deadline. Health Canada states plainly that if you miss the deadline for any reason, it must refuse your medical exemption request. That is not a discretionary refusal, it is mandatory. A missed declaration turns a medical-sale holder's fee from the exemption basis to the full 2.3 per cent revenue basis, with no appeal route. For a mid-size producer that can be a five or six figure error caused by a single unfiled form. Even licence holders with no cannabis sales are still eligible for the exemption and should still file, because the definition of sell includes offering for sale, exposing for sale and possessing for sale.

There is a narrow relief. You do not need to file for a fiscal year if, before 30 September, your licence was revoked or expired, you asked Health Canada to revoke your licence, or you notified Health Canada that you intend to cease all activities at the site. If you resume activities, you must file the exemption request immediately. After the fiscal year ends, Health Canada verifies medical-only sales using your monthly CTLS sales data, your Statement of cannabis revenue and other information, then either grants the exemption or issues an invoice.

How the fee is calculated: entry, first and subsequent years

In your entry year, which runs from your licence date to 31 March, you receive an invoice for the minimum fee for your class and pay it within 60 days. If your later Statement of cannabis revenue shows the fee should be higher, you receive a reconciliation invoice for the balance, due before 30 September of the following year. Health Canada's own example: a standard class holder reporting $3 million in entry-year revenue receives a reconciliation invoice for $46,000, which is 2.3 per cent of $3 million less the $23,000 minimum already paid.

Your first full year fee is based on the daily average of your entry-year revenue, annualized. Health Canada's example: a standard class holder that earned $3 million over 200 days of operation has a prorated revenue of $5,475,000 and a first-year fee of 2.3 per cent, or $125,925, due before 30 September. For every subsequent year the fee is calculated from the previous year's Statement of cannabis revenue and is again due before 30 September. These worked examples are why revenue reporting accuracy matters: the number you file on 30 April drives the invoice you pay on 30 September.

Statement of cannabis revenue and monthly reporting

By 30 April each year, you submit a Statement of cannabis revenue for each licensed site for the previous fiscal year, through CTLS, as long as your licence was valid for at least one day. Sales and purchases must follow generally accepted accounting principles, be reported in Canadian dollars, use discounted prices where products sold or bought at a reduced rate, and exclude taxes and pass-through remittances. You may only count cannabis purchases from other federal licence holders. Alongside this, medical-sale holders report monthly sales data in CTLS by the 10th of each month, which Health Canada uses to verify the exemption. These filing rhythms sit inside the broader Health Canada cannabis red tape reduction agenda, but the deadlines themselves have not moved.

Do not confuse the annual regulatory fee with excise duty

A frequent and costly source of confusion is treating the annual regulatory fee as if it were the same thing as cannabis excise duty. They are separate obligations, owed to different parts of government, on different timelines. The annual regulatory fee is a cost recovery charge paid to Health Canada under the Cannabis Fees Order, made under the Cannabis Act, and it funds the regulation of the cannabis industry. Excise duty is a tax administered by the Canada Revenue Agency under the excise stamping regime. Paying one does not discharge the other, and the excise duty you remit is specifically excluded from the cannabis revenue figure that drives your regulatory fee.

This matters in practice because the two systems pull your finance team in different directions. Excise reporting is monthly and product based, while the regulatory fee turns on an annual Statement of cannabis revenue and a hard 30 September deadline. A licence holder that manages excise well can still be caught out by a missed exemption declaration, because nothing in the excise process prompts it. Build the regulatory fee and exemption dates into the same compliance calendar you use for excise, controlled substance reporting and licence renewals, so a single owner is accountable for each filing and no deadline falls through the gap between finance and regulatory affairs.

Compliance checklist

Confirm which fiscal year each licensed site is in: entry, first or subsequent.
File your Statement of cannabis revenue in CTLS before 30 April for each site.
Confirm your annual regulatory fee invoice and pay it before 30 September.
If you sell only for medical purposes, file the exemption declaration in CTLS before 30 September and keep proof of submission.
Submit monthly sales data in CTLS by the 10th of each month so the exemption can be verified.
For combined medical and micro or nursery sites, confirm you are being charged the lower rate.
Diarise 30 April and 30 September every year, and set an internal reminder two weeks ahead of each.

Common mistakes

Assuming the medical exemption carries over. It must be re-filed every fiscal year.
Treating 30 September as flexible. A late exemption declaration must be refused, with no appeal.
Not filing because there were no sales. Holders with zero sales are still eligible and should still declare.
Reporting revenue with taxes or pass-through remittances included, which overstates the figure that drives your invoice.
Missing monthly CTLS sales data, which Health Canada uses to verify a medical exemption after year end.

Frequently asked questions

When are cannabis annual regulatory fees due in Canada?

The annual regulatory fee invoice is due before 30 September of each fiscal year. Your entry-year minimum fee is due within 60 days of your licence date. The Statement of cannabis revenue that drives the fee is due before 30 April.

What happens if I miss the medical exemption deadline?

Health Canada must refuse the exemption request. There is no appeal. You will then be invoiced the full annual regulatory fee, calculated as the higher of the minimum for your class or the revenue percentage. This is why the declaration should be filed well before 30 September.

How much is the cannabis annual regulatory fee?

It is the higher of the minimum fee for your class or a percentage of your cannabis revenue. The minimum is $2,500 for micro and nursery classes and $23,000 for standard classes. The percentage is 1 per cent up to $1 million and 2.3 per cent above for micro and nursery, and 2.3 per cent for standard classes.

Do I have to file the exemption if I had no sales?

Yes. Licence holders with no cannabis sales are still eligible for the medical exemption and should still file the declaration, because the definition of sell under the Cannabis Act includes offering for sale, exposing for sale and possessing for sale.

How is cannabis revenue calculated for the fee?

Cannabis revenue is the revenue from selling cannabis minus the amount paid for cannabis, following generally accepted accounting principles and reported in Canadian dollars. A negative figure is treated as zero. Exclude taxes, pass-through remittances, and revenue from transport, storage, distribution, processing, packaging, royalties, patents or leasing.

Where do I submit the declaration and revenue statement?

Both go through the Cannabis tracking and licensing system (CTLS). If you file the medical exemption in CTLS, the declaration is generated and submitted automatically. You may also submit the declaration by email using Health Canada's template.

How MFLRC can help

MFLRC supports cannabis licence holders with CTLS filing, medical-sale exemption declaration review, Statement of cannabis revenue preparation and licence-class fee modelling. We help you confirm which fiscal year each site is in, check that combined sites are charged the lower rate, and build the licensing and regulatory and quality systems that keep these deadlines from slipping. With more than 20 years across Canada's regulated sectors, our advice is senior, practical and defensible.

The 30 September deadline is close, and Health Canada cannot forgive a late medical exemption. Let us review your filings and confirm you are paying the right fee, before the date, not after the invoice.

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Conclusion

The cannabis annual regulatory fee is settled law, not a moving target, which is exactly why it is easy to overlook. The cost of a missed medical exemption declaration, though, is anything but small. Treat 30 September as immovable, file early, keep proof, and make sure the revenue number you reported on 30 April is right. If you also want to understand the separate pressure of excise duty on your margins, see our analysis of cannabis excise tax reform in Canada. Handled well, these fees are a routine annual task. Handled late, they become an avoidable and unappealable cost.