A team of investigators from the IAEA visited the bombed site earlier this year, but Damascus has rejected subsequent requests from the inspectorate to revisit the country.
The US allegations could founder if there is no evidence of a Syrian nuclear programme from the rest of the samples collected by the IAEA.
The IAEA's investigation has been complicated by the fact that the alleged reactor was not complete at the time Israeli aircraft bombed it, meaning no nuclear fuel would have been on site.
Instead of testing the site for radioactivity, the IAEA team looked for graphite, which features in the North Korean prototype that was allegedly being built.
Any major explosion, such as the Israeli bombing, would have scattered graphite over the entire site.
Months before the IAEA visit to the Syrian desert site in June, it had been covered in concrete as part of a foundation of a new building.
'North Korea link'
David Albright, a former UN nuclear inspector, said it was possible that the Israeli missiles did not disturb the tons of graphite buried in the alleged reactor.
He said judgment should be reserved until the release of results from the second batch of tests, "are more sensitive and can pick up smaller quantities".
The agency is also trying to visit three other locations suspected of hosting secret nuclear facilities, but Damascus has not granted access, citing concerns over its security.
The nuclear watchdog also wants to question Syrian officials about intelligence which appears to show years of extensive co-operation between the Syrians and North Korea.
North Korea, which exploded its first nuclear bomb in 2006, is believed by analysts to have made as many as 10 nuclear weapons before agreeing to dismantle its weapons programme last year.
Syrian officials insist that meetings between nuclear officials from Pyongyang and their Syrian counterparts are occasional and informal, diplomats say.