The IAEA analysts' conclusions are said to need further confirmation of the facts before certification.
The evidence used in the report was said to be gained from intelligence agencies and the agency's own investigations.
The analysts' report puts Iran at a further stage in the development of nuclear weapons than thought by many governments, including the US who said in 2007 that Tehran had stopped its efforts to construct such a weapon in 2003.
But the UK, France, Germany and Israel have said that Tehran has restarted work.
Washington is now re-evaluating that conclusion, a senior US official said last week.
The report, called Possible Military Dimensions of Iran's Nuclear Programme, also reportedly said that Iran had collected information on making a bomb from rogue nuclear experts and undertaken extensive research and testing on developing the components of a weapon.
However, it does not say how much progress there has been in the developing of the weapon by the Iranian defence ministry, which is said to run the programme.
The New York Times quoted the report as saying that the weapon could hit parts of the Middle East and Europe, using the Shahab missile system.
The leaking of the report could raise pressure on ElBaradei, who made the announcement on the planned inspection of the Qom nuclear facility at a joint news conference with Ali Akbar Salehi, the Iranian nuclear chief, on Sunday.
"I see that we are at a critical moment. I see that we are shifting gears from confrontation into transparency and co-operation," ElBaradei said.
"I hope and trust Iran will be helpful with our inspectors so it is possible for us to be able to assess our verification of the facility as early as possible."
Speaking from Tehran, Al Jazeera's Nazanine Moshiri reported that ElBaradei was under a lot of pressure.
"There has been some criticism that perhaps in the past Mr ElBaradei has not been as critical of Iran as perhaps some people would like him to be," she said.
"And this report ... which comes from actually inside his own organisation, saying that perhaps Iran has progressed further than what Mr ElBaradei has been saying, is extremely damning."
Muhammad Sahimi, a professor a chemical engineering at the University of Southern California, told Al Jazeera: "The confidential report of the IAEA is mostly based on the document that was supposedly on a laptop supposedly stolen from Iran in 2004.
"But the authenticity of those documents has never been established, and it is in dispute whether those documents are authentic.
"But assuming that the documents are authentic, there is still a wide gap between having the knowledge or information and actually putting that knowledge into practice."
Iran agreed to allow IAEA inspectors unfettered access to the plant during talks with the permanent members of the UN Security Council plus Germany in Geneva earlier in the week.
But the talks ended without agreement on the idea of "freeze for freeze" - a suspension of further enrichment in return for a halt to additional UN sanctions against Iran.
However, Washington conceded that the Geneva meeting, which included the highest-level direct talks between the US and Iran in three decades, marked a "constructive" start to defusing the nuclear standoff.
Western officials said Iran had agreed "in principle" to ship out most of its enriched uranium for reprocessing in Russia and France for use in an internationally supervised research reactor in Tehran.
In another development, Binyamin Netanyahu, Israel's prime minister, is reported to have handed the Kremlin a list of Russian scientists believed by the Israelis to be helping Iran to develop a nuclear warhead.
He is said to have delivered the list during a mysterious visit to Moscow with Uzi Arad, his national security adviser, last month in a private jet, the website of Britain's's Times newspaper said on Sunday.
His office claimed he was in Israel, visiting a secret military establishment at the time.
It later emerged that he was holding talks with Vladimir Putin, the Russian prime minister, and President Dmitry Medvedev.
"We have heard that Netanyahu came with a list and concrete evidence showing that Russians are helping the Iranians to develop a bomb," a source close to the Russian defence minister said last week.