Iran's belated revelation of a second uranium enrichment site has raised concerns about possible further secret nuclear sites in the country.
The International Atomic Energy Agency (IAEA) raised its fears in a report obtained by several news agencies on Monday.
The UN nuclear watchdog's report said Iran had claimed that work on the second bunkered site near Qom had started in 2007.
However, the IAEA says it has evidence the project began in 2002, was paused in 2004 and resumed in 2006.
"The agency has indicated [to Iran] that its declaration of the new facility reduces the level of confidence in the absence of other nuclear facilities under construction and gives rise to questions about whether there were any other nuclear facilities not declared to the agency," the report said.
The report is the first official document since IAEA experts inspected the Qom site last month.
The report said that the plant "corresponds to the design information provided by Iran" but that "Iran's explanation about the purpose of the facility and the chronology of its design and construction requires further clarification".
Iran revealed to the IAEA in September that it had been building a second uranium enrichment plant inside a mountain near Qom.
"The main concern in Tehran is that the IAEA is apparently mixing up its legal duties and technical duties with the political duties"
Al Jazeera correspondent
The inspectors said the plant could go live as early as 2011.
Speaking to Al Jazeera, Paul Brannan, a senior research analyst with the Washington-based Institute for Science and International Security, said: "The satellite imagery that the IAEA is looking at indicates that the tunnel entrances associated with the facility were built back in 2002.
"The satellite imagery analysis that we have done tends to support the notion that the tunnel entrances back in 2002 may not yet have been associated with the enrichment plan.
"The atomic energy organisation of Iran may have made the decision to build the enrichment plant and then may have sited it at the Qom facility.
"But nevertheless it looks like the satellite imagery shows that the construction would have begun before June 2007, which would put it at the first half of 2007 at the earliest, so that doesn't quite jibe with what Iran was telling the IAEA."
Alireza Ronaghi, Al Jazeera's correspondent in Tehran, said: "Iran plans to prove that its nuclear programme is unstoppable.
"That's why they have built this strike-proof (that's what Iran calls it) nuclear plant under the mountains near Qom to prove that Iran will never stop its nuclear programme.
"And that's a concern big enough for some of the world powers who are dealing with Iran now.
"The main concern in Tehran is that the IAEA is apparently mixing up its legal duties and technical duties with the political duties that have been imposed on it by some world powers in the [UN] Security Council.
"I have received very early reaction [to the IAEA report] from an official close to the nuclear talks in Iran.
"Iran says it has been in complete compliance with IAEA demands but will not recognise UN Security Council resolutions, and the mix up of the two, is something that worries the Iranian government very much."
The IAEA inspectors also found that Iran had recently reduced the number of centrifuges enriching uranium at its main Natanz site by 650 to 3,936, while slightly raising the total number of machines installed to 8,692.
Western diplomats and analysts said the slowdown was probably caused by technical glitches.