Marois says she will present the accord in the national assembly only when that detail has been finalized.
The premier issued the warning in Brussels while on a tour of Europe.
She insisted her stand does not put the deal in danger.
Marois pointed out there is no published text and many details still need to be worked out.
She said she is not worried.
"I promised (Prime Minister Stephen) Harper that the accord would be presented to the national assembly once Ottawa had reached a deal with our cheese producers on compensation," she said Monday. "Until we get that deal, I will not table the accord and it will not be applicable."
Marois said after a meeting with Michel Barnier, the European commissioner for internal market and services, that she sees advantages in the free-trade deal but the cheese issue had "caused some problems."
Small producers of Quebec cheese fear they could lose $450 million a year because of the European competition.
The federal government has said it will offer compensation but neither the details nor the amount have been determined.
She said Quebec is preparing to "take the lead" in advance of the implementation of the deal in the next 18 to 24 months.
"Quebec wants to position itself as a strategic partner," she told a luncheon organized by the Canada-Belgium-Luxembourg Chamber of Commerce.
The Quebec government has estimated the free-trade deal with Europe will bring the province $2.2 billion per year and create 16,000 jobs.
"Our goal is to increase our exports to Europe by 10 per cent in five years," said Marois. "There is no doubt in my mind that this new agreement will help achieve this goal."
And she said she has no doubt that an independent Quebec would continue to benefit from the deal.
"It is normal that we continue to implement the agreements that we have adopted in the legislature," Marois said, pointing out the Parti Quebecois has always supported free trade.