Iran had exceeded its stock of heavy water, a material used as a moderator in reactors such as Iran's unfinished one at Arak, for the second time since the deal was signed.
The UN nuclear watchdog said on Thursday that Iran was endangering support for a landmark deal with major powers by twice overstepping a "soft" limit on sensitive material.
A report by the International Atomic Energy Agency (IAEA) last week showed that Iran's stock of so-called heavy water had inched above the 130-metric ton level set out in the deal.
"It is important that such situations should be avoided in future in order to maintain international confidence in the implementation" of the deal, IAEA chief Yukiya Amano told the agency's board in Vienna.
Iran had slightly exceeded its heavy water limit for the second time since the deal was put in place in January, although it had not concealed the fact and had proposed remedial action.
Heavy water, a modified form of normal water, is used in certain types of nuclear reactor. Plutonium for use in nuclear weapons can be extracted from fuel rods used in heavy water reactors.
"Iran has since made preparations to transfer a quantity of heavy water out of the country," which will bring it below the ceiling, Amano said.
The July 2015 nuclear deal between Iran and six major powers places restrictions on Iran's atomic activities, monitored by the IAEA, in exchange for the lifting of international sanctions against the country.
The agreement states that Iran's "needs" are 130 metric tons of heavy water and that any excess must be "made available for export."
Last week's report said Iran had put the amount to be exported at 5 metric tons.
Amano would not say when the transfer would be made, how much heavy water would be shipped, or where to.
He also would not be drawn on whether the material had been "made available for export" as the deal requires, and as a letter sent to the agency by Iran this month said it had. "Please ask the Iranians," he said.
Reza Najafi, Iran's envoy to the IAEA, said on Thursday that Iran was "making the preparations" for doing so, telling reporters that the amount to be sold abroad may even exceed five metric tons.
US ambassador Laura Holgate urged Iran to complete the process of exporting the extra material "without delay."
"Nothing short of full implementation will assure the international community that Iran continues to uphold its commitments," Holgate told the IAEA board of governors meeting.
US President-elect Donald Trump during his campaign labelled the deal a "disaster" and threatened to tear it up.
Iran is wrong: Trump can absolutely overturn the nuclear deal. https://t.co/YTc8jHqcP9— Heritage Foundation (@Heritage) November 17, 2016