A missing Iranian nuclear scientist, who Tehran claims was abducted by the U.S., has taken refuge at a Pakistani Embassy office in Washington and is planning to return to his homeland, the State Department said Tuesday.

It was the latest development in a murky case that has been shrouded in mystery since the scientist, Shahram Amiri, disappeared while on a pilgrimage to Saudi Arabia in June 2009.

"He has been in the United States of his own free will and obviously he is free to go," department spokesman P.J. Crowley said. "In fact, he was scheduled to travel to Iran yesterday but was unable to make all of the necessary arrangements to reach Iran through transit countries."

Crowley said Amiri was at the Pakistani Embassy. "He travelled there on his own," he added, but would not elaborate. Other officials said Amiri arrived there Monday evening.

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

Crowley described Amiri as "free to come and go as he chooses," in contrast to three American hikers who have been held by Tehran since July 2009. He also raised the case of Robert Levinson, a former FBI agent who disappeared in Iran in 2007.

"We obviously continue to be mindful to the fact that we have the three hikers in custody without charge in Iran," Crowley said. "Obviously, they are there against their own free will. We also continue to have concern about others, including Robert Levinson.

"We have asked Iran many, many times for information about his whereabouts and we still do not have that information."

Iran has repeatedly claimed that the U.S. abducted Amiri — charges the Americans deny. U.S. media reported in March that the 32-year-old scientist had defected to the U.S. and was assisting the CIA in efforts to undermine Iran's disputed nuclear program.

Adding to the confusion, Amiri himself appeared in a series of videos making conflicting claims, including one where he said he was kidnapped by American and Saudi agents and taken to the U.S. and another in which he said he was freely studying in the United States.

Iran demands 'immediate' return

Iranian state television reported that Amiri entered the Pakistani Embassy's office representing Iranian interests in Washington and demanded an "immediate return" to Iran.

The Iranian interest section is technically part of Pakistan's embassy and is under Pakistani legal protection but is run by Iranians who issue visas for travellers to Iran and perform other functions.

A Pakistani diplomat in Washington said Amiri arrived at the interest section, which is separate from the main Pakistani Embassy building, at 6:30 p.m. ET Monday, and told Iranians there that he had been dropped by what he called his captors.

The diplomat spoke on condition of anonymity because he was not authorized to speak publicly. He added that Pakistani officials had yet to speak directly to Amiri.

Mostafa Rahmani, head of the Iranian office in Washington, said Amiri was there but declined to provide details.

The United Nations in early June slapped a fourth round of sanctions on Tehran over its refusal to curtail its nuclear program. Before he disappeared, Amiri worked at Tehran's Malek Ashtar University, an institution closely connected to the country's powerful Revolutionary Guard.

Iran's state TV has periodically showed purported videos of Amiri claiming abduction and torture by the U.S. Crowley, the State Department spokesman, disputed the claim of torture.

"I have no information to suggest that he has been mistreated while he has been in the United States," Crowley said.