VIENNA (Reuters) - Syria said on Friday it was cooperating fully with a U.N. inquiry into allegations of secret nuclear work in the country but would not go as far as opening up military sites because this would undermine its security.

But, faced with stiff opposition among 145 member states of the International Atomic Energy Agency, Syria dropped a bid for a seat on the IAEA's governing body, clearing the way for rival Western-backed Afghanistan to get the post, diplomats said.

The Vienna-based U.N. nuclear watchdog has been probing Syria since May over U.S. intelligence allegations that it was close to completing a secret, plutonium-producing reactor before Israel flattened the site in an air strike a year ago.

Syria -- an ally of Iran, which is the subject of a much longer-running, and now stalled, IAEA investigation -- has denied having a clandestine nuclear program. It does have one declared nuclear site -- a research reactor.

The IAEA said last week that preliminary findings from test samples taken by inspectors granted a visit to the desert location in June bore no traces of atomic activity. Syria says all that was there was a disused military building.

"We would like to underline that my government is cooperating with the agency in full transparency and will follow suit all along the way," said Ibrahim Othman, director-general of Syria's Atomic Energy Commission.

"However, this cooperation will not in any way come at the expense of exposing our military sites or causing a threat to our national security," he told the annual meeting of the IAEA's General Conference, or assembly, in Vienna.

Diplomats close to the IAEA have said Syria has ignored agency requests to check three military installations believed connected to the alleged reactor site.

SAME ISSUE STALLS IRAN PROBE

An IAEA probe into unverified intelligence about covert atomic bomb research by Iran has hit the same stumbling block -- the barring of inspectors from military sites to which the IAEA has no legal right of access without proof of nuclearization.

Iran has dismissed the intelligence, provided by 10 countries, as fabricated. The IAEA says the allegations are "serious" but Iran has not supplied evidence to refute them.

IAEA Director Mohamed ElBaradei said last week Syrian cooperation had been "good" so far but Damascus needed to show "maximum cooperation" for the agency to draw conclusions.

Western states accused Syria in the assembly of preventing full access for IAEA sleuths to documentation, officials and sites they said was needed to get to the bottom of the matter.

But ElBaradei said Israel and the United States undermined chances to arrive at the truth by, respectively, wrecking the site and taking eight months to turn over intelligence about it.

"We are in a very awkward situation because the corpse is gone. We are now in a state where we have to reconstruct a facility that is not there," he told a closed IAEA governors meeting last week. Reuters obtained a transcript of his remarks.

Syria was nominated at an Arab League summit in March for a slot reserved for the Middle East and South Asia (MESA) group on the IAEA's 35-nation governing board. Iran said it would also run for the post but withdrew on Monday in favor of ally Syria.

But a competing bid by Afghanistan prevented MESA from presenting a single nominee to the assembly for rubber-stamp approval. By Tuesday, Kabul had accumulated support from some 90 countries, a majority, including all Western states and some in Asia, Africa and Latin America, Western diplomats told Reuters.

Syria pulled out on Friday, averting a rare, polarizing vote on two candidates as well as a damaging open split in MESA. The assembly then approved Afghanistan for the governor's seat by consensus customary in non-proliferation and disarmament bodies.

"This is a victory for the IAEA's credibility," a senior Western diplomat said. "(Making Syria an IAEA governor) would have been like putting the fox in charge of the chicken coop."

(Editing by Samia Nakhoul)

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