Adm. William McRaven took the extraordinary action more than a year after the May 2011 raid in Pakistan in response to "No Easy Day," authored by former SEAL Matt Bissonnette, who tells about his participation in the operation.
In a dramatic passage, Bissonnette said that bin Laden was on the floor when he and other SEALs entered his room in the safe house in Abbottabad, having been shot by another SEAL when he had peeked his head into the hall as the team approached.
Bin Laden's body lay at the foot of the bed, twitching and convulsing, the book said, adding that the SEALs, including the author, shot him again until he was motionless.
That account differs from what U.S. officials have said publicly since the raid.
McRaven, the head of U.S. Special Operations Command, went back to the team - including the lead SEAL, or "point man" - in recent days to make sure Bissonnette did not have any information they did not know about.
Senior Pentagon officials, who declined to speak for attribution because of the sensitivity of the matter, told CNN they have now concluded Bissonnette was wrong.
Bin Laden, they said, was standing in the room when the SEALs entered and they shot him, believing he posed a direct threat, given there were weapons in the room.
Although bin Laden was unarmed, the SEALs had encountered hostile fire in the house before entering his room and he showed no signs of surrendering.
The officials CNN spoke with said it was possible Bissonnette, who was a few seconds behind the lead SEAL, never saw bin Laden standing.
It is not clear from accounts already made public if the initial shots fired by the lead SEAL - when bin Laden looked out of the room - actually hit him. One Navy official told CNN the belief is those shots missed.
Another passage causing concern in the Pentagon has been the fate of the only U.S. soldier from the war in Afghanistan currently held captive.
The parents of Army Sgt. Bowe Bergdahl were briefed on Thursday by the military about the book's contents because it contains several pages in which the author says he was on a secret mission to rescue their son.
US Army Col. Timothy Marsano, the military liaison to the family, confirmed to CNN that the Bergdahls know about the passages and are declining to comment publicly.
The book has triggered a firestorm of controversy over the author's decision to detail the bin Laden raid. Pentagon officials are also concerned that any discussion of Bergdahl, who was captured in 2009, could put him at risk.
Military officials have privately said for some time that they believe he is being held in Pakistan by members of the Haqqani network, but have not discussed details because he is still a captive.
"We are still searching for Bowe Bergdahl and any public discussion of our ongoing efforts is not helpful," one senior U.S. official said.
This official, who also spoke on the condition of not being identified, and others said the concern is insurgents might learn any detail from the book about hostage rescue techniques.
Several military officials have told CNN there was never sufficient intelligence about Bergdahl's location to mount a full rescue attempt although they conducted many searches inside Afghanistan.
But Bissonnette said there was a tip Bergdahl might be in a compound south of Kabul about a month after Bergdahl was captured and a mission ensued.
After a firefight, Bissonnette says "there was no sign of Bergdahl, but we figured he had to be somewhere nearby. There were too many fighters here, and they were well armed."