By SALMAN MASOOD and ALAN COWELL
ISLAMABAD, Pakistan - In the latest twist in a murky tale, Pakistan said Tuesday that an Iranian nuclear scientist who Tehran maintains was kidnapped by the Central Intelligence Agency had taken refuge in a section of the Pakistani Embassy in Washington that deals with Iranian interests.
Iranian officials were "making arrangements for his repatriation," said Abdul Basit, a spokesman at the Pakistan Foreign Ministry, but no details were made public.
The scientist, Shahram Amiri, 32, vanished during a pilgrimage to Saudi Arabia in June 2009, and Iran accused the United States of abducting and torturing him. He had worked at Iran's Malek Ashtar University, which is linked to the powerful Revolutionary Guards.
The United States government has never officially discussed Mr. Amiri or his disappearance, though a Western official briefed recently on evidence of Iran's nuclear program said he was "one of the sources" for new information on the program.
Mr. Basit declined to comment on how Mr. Amiri entered the embassy's Iran section and denied that the episode could strain relations between Iran and Pakistan.
"He is not in the Pakistani Embassy, per se," Mr. Basit said. "He is at the Iranian interests section, which is manned by Iranian nationals."
He added, "We understand that they are making arrangements for his repatriation." Countries that do not maintain direct diplomatic ties often establish an "interest section" in another country's embassy. Iran's is connected to the Pakistani Embassy; the United States has a parallel office at the Swiss Embassy in Tehran. Iran and the United States severed diplomatic ties after the 1979 revolution.
Confusion over the scientist deepened in June, when two conflicting videos purporting to show the scientist emerged just before the United Nations Security Council voted to approve a new set of American-backed economic sanctions against Iran over its nuclear program. The first, publicized by Iran, showed a young man speaking in Persian through a computer phone hookup and saying he had been kidnapped in a joint operation involving the C.I.A. and the Saudi intelligence service in Medina on June 3, 2009. He said that he was taken to a house in Saudi Arabia, that he was injected with a shot, and that when he awoke he was on a plane heading to the United States.
He said he recorded the video on April 5 in Tucson. The announcer said that he could not disclose how the video was obtained.
But the second videotape, posted on YouTube shortly after the first video was publicized, showed a different young man in a suit who, also speaking in Persian, identified himself as Mr. Amiri. He said he was free and safe in the United States and was working on his Ph.D. He also demanded an end to what he called false videos about himself, saying he had no interest in politics or experience in nuclear weapons programs.
If the Iranian version is true, it is not clear how the man was able to reach the Pakistani Embassy. If the second version is accurate, it is not clear why he would want to take refuge at the embassy.
Iran's state-run English-language broadcaster Press TV said the Iranian Foreign Ministry had handed over to Swiss diplomats in Tehran "new documents related to the abduction of the Iranian national by the C.I.A." and called for Mr. Amiri's "swift and unconditional release."
The broadcaster quoted an "audio message obtained by Iran's intelligence sources" as saying he had been offered $10 million "to appear on CNN and announce that he had willingly defected to the United States." Iranian news outlets have also said that a former Iranian deputy defense minister, Alireza Asgari, was abducted during a trip to Turkey in 2007. The two videos released in June served to deepen the mystery.
Salman Masood reported from Islamabad, and Alan Cowell from London.