If you do not agree with your income tax Notice of Assessment, the first step would be to call Canada Revenue Agency (CRA) to discuss the situation, and see if it can be easily resolved. See the CRA Contact Information including toll-free telephone numbers and approximate wait times.
If this does not work, you can file a notice of objection. This can be done by writing a letter to the Chief of Appeals at your tax services office, or by filing form T400A Objection - Income Tax Act.
There are time limits for filing a notice of objection.
For individuals or a graduated rate estate, the time limit is the later of:
For corporations, the notice of objection must be filed within 90 days from the mailing date of the Notice of Assessment.
The timing of filing the notice of objection is very important, even if a CRA agent implies that it is not important - see the August 2023 Life In The Tax Lane video which discusses a Tax Court Case about this.
After your notice of objection is filed, the Minister of National Revenue will notify you that it is:
File an objection - Income tax
Income tax objections decision tree
P148 Resolving Your Dispute: Objections and Appeal Rights Under the Income Tax Act - this pamphlet includes a sample Notice of Objection letter, and instructions on what information to include.
Your Rights as a Taxpayer - Taxpayer Bill of Rights / Taxpayers' Ombudsperson