San Bernardino County Sheriff's spokeswoman Jodi Miller said the remains will be identified through forensic means.
She didn't specify if the agency will use DNA testing and dental records.
A fleeing Christopher Dorner holed up in the cabin and exchanged gunfire with deputies on Tuesday afternoon.
Two deputies were shot. One later died while the other survived.
Miller said a fire erupted in the cabin. The cause of the blaze hasn't been released.
The injured deputy's current medical condition isn't known. A hospital spokewoman couldn't be reached for comment late Tuesday night and early Wednesday morning.
According to sheriff's officials, medical personnel are optimistic about the deputy's recovery but he will require additional surgeries.
In addition to the slain deputy, Dorner is also suspected of killing an Irvine couple and a Riverside police officer as part of a bloody vendetta against the LAPD. He believes the department unjustly fired him.
On Feb. 3, Irvine police found Monica Quan, 28, and her fiance, Keith Lawrence, 27, shot to death in a parked vehicle.
Quan's father is a retired LAPD captain who represented Dorner in his disciplinary hearings.
Dorner allegedly called the former captain on Feb. 7 and said he "should have done a better job of protecting his daughter," according to court documents.
Earlier that day, police said Dorner shot at an LAPD officer in Corona who was assigned to protect one of his targets. He then surfaced in Riverside and allegedly shot two Riverside police officers.
Officer Michael Crain was killed while the other officer was seriously injured.
- Ruby Gonzales