The Independent Media Center said the FBI issued an order to hosting company Rackspace "to remove physically one of our servers."
The FBI acknowledged that a subpoena had been issued but said it was at the request of Italian and Swiss authorities.
"It is not an FBI operation," FBI spokesman Joe Parris told AFP.
"Through a legal assistance treaty, the subpoena was on behalf of a third country."
The FBI spokesman said there was no US investigation but that the agency cooperated under the terms of an international treaty on law enforcement.
Rackspace, a US Web hosting company with offices in London, said it complied with a court order "pursuant to a Mutual Legal Assistance Treaty, which establishes procedures for countries to assist each other in investigations such as international terrorism, kidnapping and money laundering." The company declined to elaborate.
"The order was so short-term that Rackspace had to give away our hard drives in the UK," the Independent Media Center said.
Italian news reports said access to Indymedia had been cut as a result of an FBI operation at US and British locations.
Mauro Bulgarelli, a member of Italy's Green party, called it a "provocation and intimidate effort" against the alternative media.
The website was established by organizations during the 1999 World Trade Organization (news - web sites) protests claiming the mainstream media failed to adequately cover the news.
It calls itself "a network of collectively run media outlets for the creation of radical, accurate and passionate tellings of the truth."
Indymedia said in a statement it "had been asked last month by the FBI to remove a story about Swiss undercover police from one of the websites hosted at Rackspace."
The statement added, "It is not known, however, whether Thursday's order is related to that incident since the order was issued to Rackspace and not to Indymedia. According to Rackspace, they 'cannot provide Indymedia with any information regarding the order.'"