"There is an initial draft that we don't accept ... at the moment I have no certainty that we can reach a conclusion," the foreign affairs minister told France Inter radio on Saturday morning.
Fabius's arrival at the talks yesterday, along with the unexpected presence of US Secretary of State John Kerry, aroused speculation that agreement was near, thanks to a more flexible Iranian approach under new President Hassan Rowhani.
But on Saturday Fabius warned against a "fool's bargain", saying that Western negotiators were "not satisfied" on several points, including the construction of a "very proliferating" nuclear reactor in Arak and the question of uranium enrichment.
France, the US, Germany, the UK, China and Russia are involvd in the talks to reach an interim agreement with Iran on its nuclear programme.
Russian Foreign Affairs Minister Sergei Lavrov was due to arrive in Geneva late Saturday morning, despite having said that he would not be going to the talks on Friday.
Israel reacted to Friday's optimism by insisting that the only successful outcome would be the dismantling of Iran's nuclear programme.
France on Saturday stressed that Israel's "concerns" must be taken into account.
Fabius also told France Inter that President François Hollande would probably address the Israeli parliament, the Knesset, when he visits Israel and the Palestinian Territories on 17-19 November.
Knesset Speaker Yuli Edelstein last month said that he would not be meeting Hollande if he did not visit the parliament during his trip.