A Camp Pendleton-based sailor found dead in a guard shack at the North County military base was shot multiple times, and someone apparently tried to cover up the slaying by setting a fire, authorities confirmed today.

A suspect in the killing of 29-year-old seaman August Provost of Houston, Texas, is in military custody. The detainee, whose name was being withheld, was linked to the crime through physical evidence and statements he made, said Capt. Matt Brown, director of public affairs for Navy Region Southwest.

Despite concerns aired by gay rights activists, however, investigators have found no evidence that Provost was slain because of his sexual orientation, Brown said. According to media accounts, Provost was gay.

Those assertions are supported by statements the sailor himself made on his MySpace page. Provost was found dead at the entrance to an assault-boat compound on the western side of Camp Pendleton about 3:30 a.m. Tuesday. Two “persons of interest” were taken into custody in the case, but one has since been released, Brown said.

Despite the fact that the victim was shot, military officials have held off on specifying a cause of death, pending completion of further postmortem tests. Ben Gomez, head of the San Diego chapter of American Veterans for Equal Rights, a national advocacy group for gay and lesbian military personnel, said Wednesday that he and other local activists suspect Provost’s death was a hate crime.

Citing unnamed sources with access to a report on the seaman’s death, Gomez said Provost was killed during an argument with another sailor over the victim’s sexual orientation. The Navy spokesman, however, told reporters Provost appeared to have been a “random” victim.

Brown would not confirm or deny unsubstantiated reports that the victim’s body had been burned, saying that determination also was on hold until all autopsy findings are complete. Provost, who enlisted in the Navy in March 2008, was a member of Assault Craft Unit 5, whose personnel are assigned to duties involving hovercraft.