Besides making the admission, an internal FBI email dated 10 May 2004 also said Pentagon officials had been reminded by the FBI "of its success for many years in obtaining confessions via non-confrontational interviewing techniques".
The document was released on Monday by Senator Carl Levin, a Michigan Democrat.
Portions that had previously been blacked out were released to Levin after he and Senator Joe Lieberman, a Connecticut Democrat, asked the Justice Department to reconsider.
But substantial portions of the document remain blacked out, even in the newly released version.
Among the newly released passages was the statement that law enforcement agencies at the Guantanamo concentration camp "were of the opinion that results obtained from these interrogations were suspect at best".
This memo did not describe the interrogation techniques and did not say which results were considered suspect.
It added that the Justice Department had made its concerns known to Pentagon officials, who sometimes were at odds with the FBI over acceptable methods of interrogation at Guantanamo Bay, particularly in late 2002.
"Today we were able to obtain some information that had previously been blacked out in an FBI document critical of Department of Defence interrogation practices. As I suspected, the previously withheld information had nothing to do with protecting intelligence sources or methods, and everything to do with protecting DOD from embarrassment"
US Senator Carl Levin
At that time the military was holding what it considered high-value al-Qaida members and military officials sought permission to use interrogation techniques that were harsher than allowed under standard military practice.
Defence Secretary Donald Rumsfeld approved the use of some harsher techniques in December 2002 but rescinded the authority in January 2003 after some inside the military questioned whether they were appropriate.
Rumsfeld then convened a committee that eventually set clearer guidelines.
Another FBI email, also dated 10 May 2004, said that in weekly Justice Department meetings, officials had often discussed the military's interrogation techniques and "how they were not effective or producing intelligence that was reliable".
Both of those 10 May 2004 email messages were originally labelled secret and were addressed to Thomas Harrington, an FBI counter-terrorism expert who led a team of investigators to Guantanamo Bay.
The name of the author of the memos was blacked out.
Levin said in a statement on Monday that the newly released information highlights the fact that Justice Department attorneys had expressed concerns about the military's interrogation techniques.
"Today we were able to obtain some information that had previously been blacked out in an FBI document critical of Department of Defence (DOD) interrogation practices," Levin said.
"As I suspected, the previously withheld information had nothing to do with protecting intelligence sources or methods, and everything to do with protecting DOD from embarrassment."