Sunday's New York Times says the agencies have sought personal financial records from banks, credit card companies and other institutions.
The letters "provide tremendous leads to follow and often with which to corroborate other evidence in the context of counterespionage and counterterrorism," said Maj. Patrick Ryder, a Pentagon spokesman.
A CIA spokeswoman said her agency's use of the letters has been very limited while two military said the military has used the letters in up to 500 cases in the past five years.
Eugene Fidell, a military law expert and defense lawyer for a former Guantanamo Bay chaplain wrongly suspected of helping inmates there, told the Times he found it "disturbing" that the Pentagon could have gone through his client's bank records because the military didn't have the same civil rights protections as the FBI did.
"Where is the accountability?" he asked. "That's the evil of it. It doesn't leave fingerprints."