The information would help gauge how many terrorism investigations and intelligence warrants field offices across the United States could reasonably be expected to produce, the FBI's executive assis tant director told a closed briefing of Congress last week.
"If the numbers don't compute, that will trigger an automatic inspection from headquarters to figure out why they aren't living up to that," a senior Congressional aide told the New York Times.
"It's beyond eyebrow-raising. It seems like a bloody waste of law enforcement resources and it's pure profiling in its worst form."
Civil rights organisations and groups representing Arab-Americans agree.
"This is obviously an indication to FBI field agents that they have to view every mosque and every Muslim as a potential terrorist," Ibrahim Hooper, a spokesman for the Council on American-Islamic Relations, said. "This is really imposing a sense of siege on the Arab-American community."
The American Civil Liberties Union, one of the nation's largest civil rights groups, compared the order to the ethnic census information that was collected during the second world war. It was then used to intern Japanese-Americans.
The FBI insist that they are collecting the data in order to protect Muslims.
"The survey, a small part of the FBI's much larger re-engineering effort, looked at a wide range of demographic and other measures, focused on vulnerabilities and mosques in the past have been targeted for violence," assistant director Cassandra Chandler said.
Privately they acknowledge the move is problematic. "This is not politically correct, no doubt about it," a top FBI official told Newsweek magazine. "But it would be stupid not to look at this, given the number of criminal mosques that may be out there."
But as the FBI goes in search of Iraqi-Americans and immigrants in a bid to unearth people who might know Iraqi government officials or intelligence operatives, Arab-Americans remain sceptical.
FBI agents have been questioning them on their views on a possible war with Iraq, whether they know any Saddam Hussein loyalists and if they know of anyone who has take a suspicious trip to the Middle East recently.
"I don't think we are looking at a large population of Saddam's supporters," one senior law enforcement official said. "But you never know until you start talking to people."
Muslims in the US are already in a state of panic, as thousands of men have been forced to register in a process that has lead to the detention of more than 500 people.