The sixty-second answer
You object in writing, setting out your reasons and all relevant facts, addressed to the Chief of Appeals. The deadline is the part that catches people: an individual other than a trust gets the later of one year after the filing-due date and 90 days from the notice of assessment, but a corporation gets only the 90 days. The Minister must then reconsider and either confirm, vary or reassess, and notify you in writing. A valid objection is not defeated by the normal reassessment period closing in the meantime.
An assessment is a position, not a verdict
A notice of assessment or reassessment states the Minister's view of what you owe. Section 165 exists because that view is contestable, and it sets out the route [1].
The route is administrative before it is judicial. You object to the CRA first, and the Tax Court only becomes available after that step. Skipping it is not an option.
The deadline, which is not one deadline
Subsection 165(1) sets two different windows, and the gap between them is large enough to matter a great deal [1].
Individuals and graduated rate estates. Paragraph (1)(a) gives the later of one year after the taxpayer's filing-due date for the year, and 90 days after the day of sending of the notice of assessment [1].
Because it is the later of the two, this is generous in practice. An individual assessed shortly after filing keeps objection rights until roughly a year after the filing-due date, long after the 90 days have run.
Note the precise wording: individuals other than trusts, plus graduated rate estates. Trusts generally are expressly carved out of that category and fall into the other branch.
Everyone else. Paragraph (1)(b) allows an objection only on or before the day that is 90 days after the day of sending of the notice of assessment [1].
Corporations sit here. So do trusts other than graduated rate estates. For a corporation, the entire opportunity to disagree is 90 days measured from a letter, and it runs from the day of sending rather than the day anyone read it.
That asymmetry deserves emphasis because it cuts against intuition. An owner who has objected personally in the past, comfortably and within a year, can lose a corporate objection to a deadline they did not know had changed.
What the objection has to say
The requirement in subsection 165(1) is modest in form and substantive in content: in writing, setting out the reasons for the objection and all relevant facts [1].
Two things follow. It does not have to be elegant, and it does have to be specific. "I disagree with the assessment" states no reasons and no facts.
Large corporations face a stricter standard. Subsections 165(1.11) to (1.13) require the notice to describe each issue, specify the relief sought for each, and provide the facts and reasons relied on [1]. The practical effect is that issues not raised properly at this stage can be difficult to raise later.
Where to send it, and what happens if you get that wrong
Subsection 165(2) requires the notice to be addressed to the Chief of Appeals in a District Office or a Taxation Centre of the Canada Revenue Agency, and delivered or mailed to that office [1].
Subsection 165(6) then softens this, permitting the Minister to accept a notice of objection that was not served in the manner required [1]. That discretion is a genuine safety valve, but it is discretion, not entitlement. Sending the objection to the auditor who raised the assessment is not the same as serving it.
What the Minister must do
Subsection 165(3) puts an obligation on the other side. Once an objection has been served, the Minister must reconsider the assessment and either confirm it, vary it, or reassess, and must notify the taxpayer in writing of that action [1].
Three possible outcomes, all of which must be communicated. An objection that disappears into silence is not the design.
Two provisions that help more than they look like they do
The first is subsection 165(5), which provides that the limitations in subsections 152(4) and 152(4.01) do not apply to a reassessment made under subsection 165(3) [1].
Its practical effect is that the reassessment clock closing does not strand a valid objection. Since the normal period is three years for individuals and CCPCs, and four for other corporations [2], an objection resolved slowly could otherwise fall outside it. Subsection 165(5) removes that risk.
The second is subsection 165(7), which lets a taxpayer who has already objected appeal a subsequent assessment or reassessment to the Tax Court without serving a fresh notice of objection [1]. A reassessment issued while your objection is live does not reset you to the start.
Objecting extends your record-keeping obligation
A detail that surprises people. Subsection 230(6) requires records to be retained where an objection or a Tax Court appeal is outstanding, until the time for any further appeal has expired or the appeal has been disposed of [3].
So disputing an assessment does not start a countdown to clearing out the file. It suspends it.
The objection is only as good as the evidence
The statutory requirement is to set out the reasons and all relevant facts. Facts here means documents, and the documents in question are typically two to five years old by the time an objection is being drafted.
Most weak objections are not weak on the law. They are weak because the taxpayer is confident about a position and cannot now produce the supporting material for a specific figure on a specific line.
This is the argument for a return that stays connected to its sources. MapleTax draws figures from receipts held in MapleExpense and invoices issued through MapleInvoice, so the underlying documentation for a line remains addressable rather than archived into a general pile. Where an assessment is contested, that turns the drafting of relevant facts into a retrieval exercise.
And if the disagreement is about judgement rather than evidence - a characterisation, a reasonableness question, an allocation - that is the point at which professional advice earns its cost. The part worth doing yourself is having the documentation ready before you need to decide.