International Atomic Energy Agency Director General Yukiya Amano addressed the group's regular meeting in Vienna.
The IAEA board of governors last week backed a resolution that called on Iran to comply fully with its nuclear obligations. The U.N. nuclear watchdog had expressed frustration it wasn't granted access to some nuclear facilities in Iran, adding there may be military dimensions to aspects of Tehran's nuclear program.
Amano said the IAEA can verify nuclear material wasn't diverted specifically for military use. Iran, however, wasn't cooperating fully with inspectors.
"Therefore, we cannot conclude that all nuclear material in Iran is in peaceful activities," he said.
Amano said the IAEA was committed to dialogue with Iran to resolve outstanding issues related to its nuclear program.
Tehran maintains the nuclear program is for peaceful purposes. Iranian Supreme Leader Ali Khamenei had said that Tehran considers nuclear, chemical and similar weapons "a great and unforgivable sin."