The report includes claims Iran is planning to set up 3,000 centrifuges as it moves towards industrial-scale uranium enrichment, despite Western fears this could be used to make atomic weapons.
The confidential report by the International Atomic Energy Agency will be crucial in the UN Security Council's decision on whether to take action against Iran over its nuclear ambitions.
While Iran insists it wants to develop nuclear technology for peaceful civilian purposes, the United States claims this is a cover for the development of weapons.
"It is regrettable and a matter of concern that the... uncertainties related to the scope and nature of Iran's nuclear program have not been clarified after three years of intensive agency verifications," the IAEA said in the report, obtained by AFP ahead of its official release next week.
The report said Iran did not cooperate in the information-gathering process as much as would have been liked, and said the door is always open for Tehran to come forward.
The document has been sent to the 35 member states of the IAEA board of governors, due to meet in Vienna on March 6.
"Although the agency has not seen any diversion of nuclear material to nuclear weapons or other nuclear explosive devices, the agency is not at this point in time in a position to conclude that there are no undeclared nuclear materials or activities in Iran," said the IAEA.
The report said Iran has failed to resolve questions about the centrifuges which make enriched uranium, and about studies into missile work and a secret project for a uranium conversion plant, which are linked and could have a military dimension.
However Iran on Sunday did agree to an IAEA request to let its director of safeguards Ollie Heinonen to meet with a military officer connected with these projects in Tehran, an interview the IAEA has been requesting for over a year.
The IAEA has called on Iran to suspend its uranium enrichment work but Iran is pushing ahead with this work, and had fed a 10-centrifuge cascade on February 15 with the uranium gas that is processed into enriched uranium, which can also be fuel for nuclear power reactors.
Iran has tested a 20-machine cascade that is now ready for the feeding of the uranium gas.
These cascades can not make enough enriched uranium to make an atomic bomb but Western diplomats have said that running them will give Iran the knowledge to eventually make industrial amounts of enriched uranium.
Talks set to resume
A senior Russian official told AFP that an Iranian delegation, led by Ali Hosseini-Tash, will be in Moscow on Tuesday for talks with the Russian security council on a Russian plan, backed by the West, that aims to defuse tensions over Iran's nuclear plan.
Word of the fresh negotiations comes a day after Iran announced it had reached an agreement in principle with Russia on a plan under which the two countries would set up a joint venture on Russian territory for enrichment of uranium to be used in Iran's first nuclear power station.
But Russian officials quickly poured cold water on the claim by Tehran that a deal had been reached.
And the US reacted warily to the possible Russia-brokered deal, saying that the Islamic republic "cannot be trusted."
Washington said Iran has a one-week opportunity before the March 6 IAEA meeting in which to ease fears that it is seeking atomic weapons.
"We've said that during this time the regime in Iran has an opportunity to change their ways and change their behaviour when it comes to the nuclear program," said White House spokesman Scott McClellan.