The UN's nuclear watchdog has said traces of uranium taken from the site of an alleged nuclear reactor in Syria were manmade and rejected the Syrian government's claim that it came from an Israeli air strike that destroyed the site in 2007.

The report by the International Atomic Energy Agency (IAEA) on the Dair Alzour site puts strong pressure on Damascus as it rejects the Syrian explanation for the presence of uranium and denounces the government for its lack of cooperation with the agency's inquiry.

The IAEA says Israel also failed to cooperate, but its findings give weight to the Israeli and US allegation that Dair Alzour was a secret reactor intended for eventual production of weapons. The report explicitly questions Syria's denials.

"Syria has stated that the origin of the uranium particles was the missiles used to destroy the building," the IAEA report says. "The agency's current assessment is that there is a low probability that the uranium was introduced by the use of missiles as the isotopic and chemical composition and the morphology of the particles are all inconsistent with what would be expected from the use of uranium-based munitions."

The report says that after an initial visit in June 2008, which revealed the presence of processed uranium, IAEA inspectors had not been allowed back to Dair Alzour and other sites where debris might have been stored, on the grounds they were "military installations".

Experts at the agency's Vienna headquarters carried out further analysis of the original samples and found more traces of uranium.

"These uranium particles … are of a type not included in Syria's declared inventory of nuclear material," the report says. It pointedly requests "clarification of efforts by Syrian entities to procure materials and equipment which could support the construction and operation of a nuclear reactor".

The report says Damascus replied to some questions put to it about Dair Alzour by IAEA inspectors but is damning in its assessment of the quality of the Syrian responses, saying they "were only partial and included information already provided to the agency, and did not address most of the questions raised in the agency's communications".