Modesto police spokesman Chris Adams says the body was found Friday in the rubble of the home, where a raging fire had broken out overnight. Police had waited for clearance from fire officials before entering.
The fire erupted during a daylong standoff with a man who police say opened fire as authorities tried to serve an eviction notice. They say the suspect killed a Stanislaus County sheriff's deputy and a civilian before holing up inside the apartment.
Adams says it'll take days or weeks to identify the body, which was charred from the fire.
The blaze was put out by firefighters shortly before 2 a.m. Friday.
The shooting led to a standoff with the suspect. More than 100 law enforcement officers were at the scene. FBI and SWAT teams surrounded the building and authorities evacuated nearby residents while others remained in their homes.
It was not clear how the fire began, but officials reportedly acknowledged that a combination of flash-bang devices and tear gas could have been responsible.
Officials identified the deputy killed as 53-year-old Robert Paris, a 16-year veteran of the Stanislaus County Sheriff's Department. The name of the civilian has not been released.
The Associated Press contributed to this report.