The report, to be delivered as early as Thursday to a board meeting of the International Atomic Energy Agency, also said the Islamic republic received sensitive technology that can be used as part of a weapons programme earlier than it originally said it did.
While not proving or disproving that Iran had weapons ambitions, the details are significant as the agency tries to piece together the puzzle of nearly 18 years of a clandestine nuclear programme first revealed in February 2002.
Marked "highly confidential", the report to the UN nuclear monitor was made available on Wednesday by a diplomat accredited to the agency who demanded anonymity because he is not authorised to release such information to the media.
The three-page report took stock of the present stage of a more-than-three-year probe of Iran's nuclear activities.
It suggested that some of the investigations were stalled, saying: "the agency still needs to understand" the nature, dates and number of contacts between Iranian officials and nuclear black market intermediaries that supplied Tehran with much of its advanced technology - including centrifuges for uranium enrichment.
Shortly after details of the report were revealed, Iran's former president Hashemi Rafsanjani, the front-runner in the country's presidential race, acknowledged Tehran may in the past have deceived the IAEA and the world.
But he told BBC television that Iran had "made everything transparent" since the start of the IAEA's investigations.
The IAEA first revealed that Iran produced small amounts of plutonium as part of covert nuclear activities in November 2003, more than a year after revelations that Iran had run a secret atomic programme led the agency to start investigating the country.
A confidential European Union briefing note made available to The Associated Press cited the Saudi deputy foreign affairs minister, Prince Turki bin Mohammed bin Saud al-Kabira, as telling European envoys on the weekend that "Iran should cooperate for the safety of the whole region" in ensuring its nuclear aims were peaceful.
Frontrunner Rafsanjani says Iran
has introduced transparency
Much of the country's nuclear programme came from the network headed by Pakistani scientist AQ Khan, including the initial technology used in uranium enrichment.
Iran froze enrichment late last year as it started talks with France, Britain and Germany meant to reduce concerns about Tehran's nuclear ambitions.
The UN nuclear watchdog is pushing Iran to cooperate more with nuclear investigators, and agency chief Mohamed ElBaradei told board members on Tuesday that more information was needed about Iran's uranium enrichment programme.