A spokesman from Pakistan's Foreign Office, Abdul Basit, told the BBC that Shahram Amiri was seeking immediate repatriation to Iran.
In June videos purportedly of Mr Amiri but containing contradictory information on his whereabouts emerged.
The US rejected Tehran's claims that it was behind Mr Amiri's disappearance.
Iranian media say Mr Amiri worked as a researcher at a university in Tehran, but some reports say he worked for the country's atomic energy organisation and had in-depth knowledge of its controversial nuclear programme.
ABC News reported in March that he had defected and was helping the CIA, revealing valuable information about the Iranian nuclear programme.
But earlier this month, Tehran said it had proof he was being held in the US.
The allegation came after three videos purportedly of Mr Amiri emerged - the first said he had been kidnapped, the second that he was living freely in Arizona, and the third that he had escaped from his captors.
The BBC's former correspondent in Tehran, Jon Leyne, says that Iran's version of the story seems to be backed up by events unfolding in Washington DC.
Our correspondent says Mr Amiri's sudden appearance is a major embarrassment for the American spy agencies and could lead to a diplomatic stand-off.
Analysis: Jon Leyne, former BBC Tehran correspondent
"There are two diametrically opposed versions of the Shahram Amiri story. Iran says he was kidnapped. American sources said that he defected and was spilling the beans on the Iranian nuclear programme.
On the face of it, the Iranian version now sounds a lot more credible. However those inclined to give the US the benefit of the doubt will point out that it is still conceivable that Mr Amiri was persuaded, blackmailed, or even conceivably kidnapped by the Iranians themselves back into their hands.
Either way this is a big embarrassment for the American spy agencies, who have let slip a man they had been building up as a major catch."
According to Mr Basit in Pakistan, the head of Iran's interest section, Dr Mostafa Rahmani, is planning to repatriate the scientist back to his country.
But while US authorities cannot enter Iran's diplomatic premises, they could prevent Mr Amiri leaving.
The Iran interest section is housed in Pakistan's embassy in Washington, but run by Iranians. The US cut diplomatic relations with Iran shortly after the 1979 Islamic Revolution.
Mr Amiri went missing a year ago while on pilgrimage in Saudi Arabia.
The first two videos, telling starkly contradictory stories, were posted on the video-sharing site YouTube on 8 June.
In the first, initially broadcast by Iranian television, a man purporting to be Mr Amiri says he was kidnapped by the US while on pilgrimage in the Saudi Arabian city of Medina and that he is now living in the US state of Arizona.
At the time the Iranian government described the video as evidence that he was being held in the US against his will.
In the second, posted hours later on YouTube, a similar-looking man claiming to be the scientist says he is happy in the US, living in freedom and safety.
Plea for help
In the third video, which was broadcast by Iranian state TV on 29 June, a man claiming to be the missing scientist says: "I, Shahram Amiri, am a national of the Islamic Republic of Iran and a few minutes ago I succeeded in escaping US security agents in Virginia.
In the most recent video the man claims to have escaped US custody:
"Presently, I am producing this video in a safe place. I could be rearrested at any time."
The man in the video also dismisses the second recording, in which it was claimed that the scientist was living freely in the US, as "a complete fabrication".
"I am not free here and I am not permitted to contact my family. If something happens and I do not return home alive, the US government will be responsible."
The video finishes with the man urging Iranian officials and human rights organisations to "put pressure on the US government for my release and return".
"I was not prepared to betray my country under any kind of threats or bribery by the US government," he adds.