Iran has failed to answer questions about its nuclear programme, just weeks before a deadline for a deal with international powers, the IAEA said in a confidential report, according to the BBC.
While Iran has complied with an agreement to curb uranium, the global energy agency said it has made no progress in its investigation into possible military dimensions of the programme.
US Secretary of State is set to meet with Iranian Foreign Minister Javad Zarif for talks in Oman this weekend.
The latest report from the International Atomic Energy Agency could reduce the chances of a deal between Iran and world powers, as it had promised to cooperate fully with the agency.
Tehran has always denied the charge, levelled by world powers, that it is seeking to develop nuclear weapons.
"Iran has not provided any explanations that enable the energy agency to clarify the outstanding practical measures," the IAEA said, as quoted by the BBC.
While the IAEA investigation is separate to the negotiations with world powers including the US and the EU, the allegations of nuclear weapons development are a key issue for the international community.