Ayham al-Samarraie, a Sunni Arab who served in the first post-war interim government of Iyad Allawi, had been in Iraqi custody since his arrest on charges of financial and managerial corruption in August.
A source in the prime minister's office said US officials had taken him from the courtroom at the central criminal court in Baghdad after sentencing.
"I am under American protection," al-Samarraie told Reuters by telephone, without explaining how he had managed to leave the court. In an earlier call, he said he was at the US embassy.
An embassy official, who declined to be named, denied he was at the mission, situated in the sprawling, heavily fortified Green Zone, entry into which is tightly controlled.
If al-Samarraie's presence is confirmed, it could be politically embarrassing for the Americans, who have repeatedly stressed the independence of the Iraqi judiciary.
It would also raise questions about the sovereignty of the Iraqi government, which has sought to show Iraqis it is independent of American influence.
"In the absence of a Privacy Act waiver, US federal law prohibits us from providing information on US citizens," US embassy spokesman Lou Fintor told Reuters.
Sabah al-Saedi, from the powerful Shia Alliance party, protested against what he called "American interference in Iraqi judicial law" and said the government must take steps to prevent al-Samarraie being taken out of the country.
Al-Samarraie however described the guilty verdict in his trial as political and said he had sought American protection because he feared for his life.
"If I get out, they will kill me in two minutes," he said.
Al-Samarraie, a former Baath party member, who defected and spent years in exile in the United States, said he was being victimised because of his opposition to Shia militias, who are accused of killing hundreds of members of his sect.
But a spokesman for Iraqi Commission for Public Integrity, a government body that investigates corruption in Iraq's ministries, denied any political motive in the case.
"This is not true. The court listened to witnesses and has evidence. He faces six cases of managerial and financial corruption and this was just one of them. He is due back in court in a few days for another case," spokesman Ali al-Shaboot said.
Details of the cases are sketchy. Al-Sammarraie would only say he had been accused of wasting public money by buying an electricity generator worth $200,000 for a neighbourhood in Amara, capital of the southern Maysan province.
Corruption is rampant at every level of the government and has cost the state billions of dollars and al-Maliki, the prime minister, has made tackling it a priority.
On Sunday, the Iraqi parliament voted to remove the immunity from prosecution of Sunni Arab lawmaker Mishaan al-Jubouri, who is accused by anti-corruption investigators of pocketing millions of dollars while in charge of protecting northern oil pipelines.
Al-Jubouri said the charges were fabricated by the dominant- Shia government in revenge for his opposition to growing Iranian influence in Iraq.