U.S. State Secretary Hillary Clinton said on Tuesday that the Iranian nuclear scientist who claimed being kidnapped by U.S. agents is free to go.

"Mr. Amiri has been in the United States of his own free will and he is free to go," Clinton told reporters, officially admitting for the first time that the scientist was in the U.S. and declining charges that he was held here against his will.

Clinton said whether he stays in the U.S. "are decisions that are his alone to make."

The Iranian nuclear scientist, named Shahram Amiri, went missing while on a pilgrimage to Saudi Arabia in June 2009.

He arrived at the Pakistani Embassy compound in Washington on Monday and asked to go home. Iran maintains an interests section in the Pakistani Embassy because U.S. broke diplomatic relations with Iran following Iran hostage crisis in 1980.

Iran has accused the U.S. of kidnapping Amiri, a charge denied by the U.S.

The situation has become confusing as Amiri appeared in several videos in recent months, making conflicting claims about what happened.

In one video clip, he claimed he was snatched by U.S. and Saudi agents. But in another, he said he was happily studying in the U.S. In March, media reports said he defected and was helping the U.S. intelligence organization.