The state TV says the scientist, Shahram Amiri, entered the embassy's office representing Iranian interests in the US and demanded an "immediate return" to Iran.
Mostafa Rahmani, head of the Iranian office in Washington, says the report is true.
Rahmani said Iran's foreign ministry will "release details later."
Amiri, a university researcher working for Iran's Atomic Energy Organization, disappeared during a pilgrimage to Saudi Arabia a year ago and Tehran accused Riyadh of handing him over to the United States, which Saudi Arabia and the US has denied.
Iran's state radio said: "A few hours ago Shahram Amiri took refuge at Iran's interest section at the Pakistan Embassy in Washington, wanting to return to Iran immediately."
Iran and the United States cut diplomatic relations shortly after the country's 1979 Islamic revolution. The Pakistani Embassy looks after Iran's interests in the United States.
Iran summoned the Swiss ambassador to Tehran earlier this month and handed over documents which it said showed Amiri had been kidnapped by the United States.
US interests in Tehran are handled by the Swiss Embassy.
Confusing video footage of Amiri has been aired in the past weeks. In one video, a man identified as Amiri, said he had been taken to the United States and tortured.
In another video that appeared on the Internet, a man also purporting to be the scientist said he was actually studying in the United States.
In a third video, a man describing himself as Amiri said he had fled from US "agents" and was in hiding, urging human rights groups to help him return to Iran.
In March, ABC news said Amiri had defected to the United States and was helping the CIA.
Tehran initially refused to acknowledge Amiri's involvement in Iran's disputed nuclear program, which the West fears is being used to develop nuclear weapons. Iran says it is aimed at generating electricity.
