"The information available to the agency … raises concerns about the possible existence in Iran of past or current undisclosed activities related to the development of a nuclear payload for a missile," the watchdog's chief Yukiya Amano wrote in his first report to its board of governors.
It was the first time the Vienna-based International Atomic Energy Agency (IAEA) had expressed such concern about Iran's "current" activities.
The report also confirmed that Tehran had begun enriching uranium at higher levels, theoretically bringing it closer to levels needed for making an atomic bomb.
"Iran provided the agency with mass spectrometry results which indicate that enrichment levels of up to 19.8 percent (uranium) were obtained," the report said.
The enrichment was carried out at a plant in Natanz between February 9 and 11.
Iran has so far enriched uranium to levels of no more than 5.0 percent at Natanz, in defiance of UN orders for it to cease and three rounds of UN sanctions.
But earlier this month, Iran announced it would begin enriching uranium to 20 percent, ostensibly to make the fuel for a research reactor that makes medical radioisotopes.