"CETA is done and we will not reopen it," said EU Trade Commissioner Cecilia Malmstrom.
Ms Malmstrom was speaking as EU trade ministers met in Slovakia to discuss CETA and a similar deal with the US, TTIP, which has also faced criticism.
A draft CETA deal has been agreed, but parliaments could still delay it.
Thousands of activists protested against CETA and TTIP in Germany on Saturday and thousands more in Brussels - outside the EU's headquarters - on Tuesday.
Activists fear that the deals could water down European standards in the key areas of workers' rights, public health and the environment.
There is also great anxiety about proposed special courts where investors will be able to sue governments if they feel that legislation hurts their business unfairly.
Critics say the mere existence of such courts - an alternative to national courts - will have a "chilling" effect on policymakers, leading to slacker regulation on the environment and welfare.
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Ms Malmstrom said CETA would dominate Friday's meeting in Bratislava. The Commission hopes the deal can be signed with Canada at the end of October, so that it can then go to the European Parliament for ratification. But it will also need to be ratified by national parliaments across the EU.
"What we are discussing with the Canadians is if we should make some clarifications, a declaration so that we can cover some of those concerns," Ms Malmstrom said.
She acknowledged fears in some countries that politicians might see their "the right to regulate" diluted. "Maybe that [right] needs to be even clearer in a declaration," she said, admitting that the CETA negotiations were still "difficult".
Karoline Graswander-Hainz, an Austrian Socialist MEP, said the EU's top court - the European Court of Justice - must first examine the proposed Investment Court System (ICS) to check its legality.
CETA holds "great risks" for Europe, she warned, adding that some of her fellow MEPs thought likewise.
German Vice-Chancellor and Economy Minister Sigmar Gabriel called CETA "a model for future deals".
But he was pessimistic about TTIP. "The Americans were not prepared to make Europe offers that Canada made, and so there will definitely not be a [TTIP] deal this year," he said.
Supporters of CETA and TTIP say such deals could set global trade standards, warning that failure could mean China setting the standards.
CETA and TTIP promise to remove tariffs and non-tariff barriers, boosting growth on both sides of the Atlantic, free trade advocates say.
The European Commission has ruled that a controversial EU-Canada free trade deal - CETA - cannot be renegotiated, despite much opposition in Europe.