The UN agency said that Iran has not yet disproved allegations that its nuclear activities are for military purposes.
"Substantive explanations are required from Iran to support its statements on the alleged studies and on other information with a possible military dimension," its report said.
The IAEA said that "Iran has not provided the agency with all the information, access to documents and access to individuals necessary to support Iran's statements."
"The agency is of the view that Iran may have additional information, in particular on high explosives testing and missile-related activities, which could shed more light on the nature of these alleged studies and which Iran should share with agency," its report said.
Gregory Schulte, the United States envoy to the IAEA, said Iran was blocking the IAEA's efforts to investigate indications that it had engaged in studies, engineering work, and procurement relevant to building nuclear weapons.
"The report shows in great detail how much Iran needs to explain, and how little it has," he said.
A European diplomat said: "Altogether this report is a clear vote that Iran could have done more, but that it didn't.”
In Tehran, a senior Iranian official said on Monday the report showed that Iran's nuclear programme was peaceful, the semi-official Fars News Agency reported.
The report from the International Atomic Energy Agency (IAEA) "is another document that shows Iran's entire nuclear activities are peaceful", Ali Asghar Soltanieh, Iran's ambassador to the Vienna-based agency, said according to Fars.
"Once more it has been explicitly underlined that there has been absolutely no evidence regarding the diversion of Iran's nuclear activities or materials toward military purposes," he said.