Speaking to France Inter radio from the Swiss city as a third day of talks opened, Fabius also pointed to a need to take into account "concerns" from Israel.
"There is an initial draft that we do not accept... As we speak, I have no certainty that we can finish up," Fabius said.
"There are some points on which we are not satisfied," the minister said, citing the "extremely prolific" Arak nuclear reactor and the question of uranium enrichment.
"There's a whole stockpile enriched to 20 percent. That's a lot. How can this stockpile go back down to five percent, which is less dangerous?" he asked.
Western powers suspect Tehran of enriching uranium to build a nuclear bomb. Iran denies the charge, insisting its programme is peaceful.
"If these questions are not settled, it will not be possible," Fabius said, insisting that he wanted an agreement but warning against being duped.
He added: "It is necessary to take fully into account Israel's security concerns and those of the region."
Israel has warned against a deal with Iran and reaffirmed its right to ensure its own security.
The United States, France, Britain, Russia, China and Germany are holding talks with Iran in Geneva in a bid to reach a landmark deal on Tehran's nuclear programme.