Gannett is asking a court to cancel the subpoena, saying it breaches the first amendment of the US constitution, which protects the free press from government interference.
“Being forced to tell the government who reads what on our websites is a clear violation of the first amendment,” said Maribel Perez Wadsworth, USA Today’s publisher.
“The FBI’s subpoena asks for private information about readers of our journalism.”
Ms Wadsworth said the the FBI’s order broke the justice department’s guidelines on the “narrow circumstances” in which the government can subpoena reporters.
Although Gannett’s lawyers had tried to contact the FBI, the agency had not provided it with an explanation for the subpoena, she added.
Gannett’s lawyers say the order is “unconstitutional”, and invades the rights of both the news organisation and its readers, citing a Supreme Court judgement that said: “A requirement that a publisher disclose the identity of those who buy his books, pamphlets or papers is indeed the beginning of surveillance of the press”.