WASHINGTON – An Iranian scientist sought refuge in the Pakistani Embassy compound and asked to go home, an apparent defection gone wrong that could embarrass the U.S. and its efforts to gather intelligence on Tehran’s suspected nuclear weapons program.

Iran — and at one point, scientist Shahram Amiri — claimed the CIA had kidnapped him; the U.S. said Tuesday that nothing of the sort happened. Amiri disappeared while on a pilgrimage to Saudi Arabia in June 2009, surfacing in videos but otherwise out of sight until the latest bizarre twist in the case.

“Mr. Amiri has been in the United States of his own free will and he is free to go,” Secretary of State Hillary Clinton said. It was the first time the Obama administration publicly acknowledged Amiri was in the U.S.

Reliable and timely information about Iran’s nuclear program is of enormous importance to the Obama administration and other countries seeking to stop the Islamic republic from getting the bomb. Beyond using diplomatic means to try to stop Iran, the U.S. and Israel have not ruled out using military force.

Iran says that its nuclear program is for peaceful purposes.

The U.S. has denied Iran’s accusation that U.S. agents kidnapped Amiri — a charge that grew more confused with the appearance in recent months of videos purporting to show Amiri making conflicting claims about his fate.

“He left his family behind, that was his choice,” said a U.S. official who was briefed on the case and spoke on the condition of anonymity because the official wasn’t authorized to speak publicly about the case.

In one, he claimed U.S. and Saudi “terror and kidnap teams” snatched him; in another, he said he was happily studying for a doctorate in the U.S. The murky circumstances gave credence to the theory that Amiri, 32, might have been coerced by Iran into claiming he was kidnapped.

“I expect they got to his family,” said Clare Lopez, senior fellow at the Center for Security Policy and a former operations officer for the CIA. “Now he’ll go back and save them.” ABC News reported that Amiri called home earlier this year because he missed his wife and son in Iran and that his son had been threatened with harm.

Whatever the reason for his disappearance, important questions remain about what of value — if anything — Amiri shared with American intelligence about the Iranian nuclear program.

State Department spokesman P.J. Crowley said he does not know what Amiri may have told U.S. officials, but he did say that the U.S. government “has maintained contact with him” during his stay in the U.S. Pressed to say whether Amiri was a defector, Crowley replied, “I just don’t know the answer.”

Iran’s foreign minister, Manouchehr Mottaki, told a news conference in Madrid that Amiri was found after having been kidnapped during the Saudi Hajj and taken to the U.S. against his will. He demanded that Amiri be allowed to return home “without any obstacle.”