Can I still claim the capital gains exemption if my accountant made an error on an earlier corporate filing?

It depends entirely on what the error actually was, not on the fact that an error happened. If it was a purely administrative or reporting mistake that doesn't touch the substantive facts the exemption depends on — how the corporation's assets were actually used, whether it was Canadian-controlled, how long shares were held — it likely doesn't affect your eligibility today, though it may still be worth correcting through an amended return before or alongside the sale so your filing history is clean and consistent.

If the error actually affected something the qualifying tests look at directly — for example, a filing that misstated the corporation's asset composition, or something bearing on its status as Canadian-controlled during the relevant period — that's a more serious issue, since the CRA's review of an exemption claim can look back at exactly that kind of history. It doesn't automatically mean you can't claim the exemption, but it means the error needs to be understood, and likely corrected, before you rely on qualification with confidence.

Getting your accountant (or a new one, if trust in the original filing is part of the concern) to review exactly what happened and its actual effect on qualification is the necessary first step before finalizing a sale.