FBI director Robert Mueller defended the agency's use of informants within US mosques amid complaints that worshippers and clerics were being targeted instead of possible terrorists.
Mr Mueller's comments came days after a Michigan Muslim organisation asked the US Justice Department to investigate complaints that the FBI was asking the faithful to spy on Islamic leaders and worshippers.
Similar alarm followed the disclosure earlier this year that the FBI planted a spy in Southern California mosques.
"We don't investigate places, we investigate individuals," Mr Mueller said during a brief meeting with reporters in Los Angeles.
"To the extent that there may be evidence or other information of criminal wrongdoings, then we will ... undertake those investigations. We will continue to do it."
He called relations with US Muslims "very good", but acknowledged there were disagreements.
The Council of Islamic Organisations of Michigan sent a letter to US attorney general Eric Holder after mosques and other groups said members of the community had been asked to monitor people coming to mosques and donations they made. The FBI's Detroit office has denied the claims.
In the California case, information about the informant who spied on the Islamic Centre of Irvine came out at a February detention hearing for a brother-in-law of Osama bin Laden's bodyguard, an Afghan native and naturalised US citizen, Ahmadullah Niazi, who is accused of lying on his citizenship and passport applications about terrorism ties.
Community leaders said they suspected since at least 2006 that the FBI was trying to infiltrate Muslim organisations in the area.
"History disputes Mr Mueller's statements, at least in Southern California," said Shakeel Syed, executive of the Islamic Shura Council of Southern California.
"It doesn't alleviate anything. It only continues to show the sheer arrogance demonstrated by the bureau in holding Muslim community members, clerics, mosques, as suspects."
Mr Syed is among community leaders in court seeking government records of surveillance.
FBI agents and prosecutors say spying on mosques is one of the best weapons to uncover lurking terrorists or threats to national security, but it has posed a politically and legally thorny issue with Muslims who see themselves as unjustly monitored.
"The FBI needs to do what it needs to do, certainly," Mr Syed said. But he said the agency was "trying to incite and entrap" law-abiding people.
Mr Mueller also said that there would be no change in the FBI's priorities in the new administration.
"I would not expect that we would in any way take our foot off the pedal of addressing counter-terrorism," he said.
"My expectation is that we'll see an uptick in terms of resources devoted towards our domestic criminal responsibilities, but we will not ... relax our responsibilities when it come to counter-terrorism or counter-intelligence."Reuse content