However, Mottaki said that Tehran could still be prepared to directly exchange the low-enriched uranium for processed nuclear fuel, providing the swap took place on Iranian soil.
"It means that we will [instead] consider swapping the [nuclear] fuel simultaneously in Iran," he said.
The deal was seen internationally as a confidence-building measure for Iran, which wants to prove to the world that its nuclear programme is not intended for making weapons.
France said that the Iranian remarks were "extremely negative", but pledged to continue negotiations.
"There is a clear and negative response from the Iranians," Bernard Kouchner, the French foreign minister, said.
The deal had been negotiated between Iran and the five permanent United Nations Security Council members, plus Germany.
The West believes the plan would leave the Islamic republic without sufficient material to make a nuclear weapon, at least from stockpiles known to the international community.
Mottaki also said the Islamic republic was ready for another round of talks with world powers over securing fuel for its Tehran research reactor. The first meeting was held in Vienna on October 19.
"We have called for another meeting of the technical people who were part of Vienna talks and we will explain our considerations. But so far such meeting has not convened," Mottaki said.
The United States rejected earlier Iranian calls for amendments and further talks on the deal and Barack Obama, the US president, said that time was running out for diplomacy to resolve the issue.