Islam Times reports from Press TV: "We are not saying that Iran has a nuclear weapons program. We have concerns and we want to clarify the matter," Yukiya Amano was quoted by Reuters as saying on Monday.
He made the remarks at the opening session of the IAEA Board of Governors meeting in Vienna, Austria on Monday.
"Full implementation by Iran of its binding obligations is needed to establish international confidence in the exclusively peaceful nature of Iran's nuclear program," Amano said.
This is while the UN nuclear agency in its latest report in February reaffirmed that Iran's nuclear program has never been diverted to nuclear weapons production.
All reports the IAEA has so far issued on Tehran's nuclear activities verify that there has been no diversion in the country's civilian nuclear program.
In February, the US National Intelligence Estimate reiterated its 2007 position that US spy agencies have concluded that Iran is not after nuclear weapons.
Iran says its nuclear program is solely aimed at peaceful purposes, but Washington and its allies have repeatedly accused Tehran of pursuing a military nuclear program.
The Islamic Republic says that as a member of the IAEA and a signatory to the Nuclear Non-Proliferation Treaty, it has the right to use peaceful nuclear energy.