An INC official on Tuesday confirmed the order which came just days after a US-appointed Iraqi judge issued a warrant against party leader Ahmad Chalabi and his nephew Salim Chalabi.
Spokesman Haidar Musawi said: "A US patrol came and handed us an order from the prime minister's office to evacuate our Baghdad headquarters.
"This is part of the government's campaign against us and the patriots of this country."
Chalabi told Aljazeera the accusations against him were "silly".
"The judge is a fresh graduate of law who was appointed by Bremer who made him [a] first-class judge and was keen to attack me, my family and my nephew Salim Chalabi," he said.
Currently in Iran, he added that he would go back to Iraq to defend himself.
Chalabi, who founded the INC as an opposition group to Saddam Hussein and was previously funded by the Pentagon, was tipped to lead post-Saddam Iraq, but his influence waned after his ties with Washington soured.
Arrest warrants were recently issued against Chalabi in connection with counterfeiting money and against his nephew Salim for murder.
Both men deny the charges.
The INC took over the former intelligence headquarters in Baghdad after the US-led invasion last year.
A host of other Iraqi parties occupy buildings and property that housed the security and government apparatus of the former ruling Baath party.