Kevin Collier, 32, texted friends and family on Sunday that he had killed his daughter and mother-in-law, police spokesman Lt. Mark Coit said.
The baby was found inside the truck with a gunshot wound to the head, and authorities were trying to determine whether the girl was Collier's 1-year-old daughter, Rhilee, Colt said.
Authorities believe she was killed before police arrived.
Collier's mother-in-law, 51-year-old Beverly Rakov, remained missing as investigators combed the charred debris of the home in El Cajon, a working-class city east of San Diego.
Heather Gooden, a friend of Rakov, said she received a message early Sunday in which Rakov said her son-in-law had guns and she feared for her life.
Meanwhile, El Cajon Officer Jarred Slocum, 28, remained hospitalized in critical but stable condition after undergoing surgery for a gunshot wound to his forehead that fractured his skull.
Slocum was responding to a call shortly after 5 p.m. Sunday that a gunman had set a home on fire. When Slocum approached the dwelling, he was shot by someone inside the house, Coit said.
The 4-year Police Department veteran fired before grabbing his neck and falling against a chain link fence. His rookie partner, Tim McFarland, ran to drag him to cover, assisted by two neighbors.
Smoke billowed from the home. Helicopters dumped water overhead to control the blaze as SWAT team members surrounded the property and officials evacuated nearby homes and shut down surrounding roads and freeways, unsure whether the gunman had escaped.
As the flames eased, firefighters moved in to the home, protected by gun-wielding SWAT officers.
They found the body of an adult near the front of the home's interior, the head and shoulders protruding from the burning debris. Police believe it may be that of Collier, but Coit said dental records may be needed to confirm the sex and identity because of the body's condition.
Police believe Collier died in the blaze because authorities had sealed off the area and he was not found.
Coit said Collier's wife managed to escape and was safe. Police were checking on whether there had been any prior domestic disputes reported at the home.
The stench of smoke early Monday still wafted through the neighborhood of lower- to middle-class older homes in the San Diego suburb, as bewildered neighbors stared at the blackened home in disbelief.
Gooden, 41, arrived sobbing at the police tape cordoning off the homes. She said she has known the family for 30 years and never heard of any problems with violence.
Gooden said Rakov owned the home, and Rakov's daughter, Alyssa, and her husband and baby daughter had moved in with Rakov after a job opportunity for Collier in New York fell through in December. She said she heard the couple had filed for divorce last week.
Gooden said she texted Rakov shortly before 8 a.m. Sunday to see if she could pick up her daughter's furniture that Rakov was storing for her.
Rakov texted back that she couldn't do it because her son-in-law had taken her grandchild and police were at her home.
Then she wrote a chilling final message: "I have never been so scared in my life, Heather. He has guns. He's gonna shoot my daughter. (H)e has lost his (expletive) mind."
Gooden sent repeated texts to Rakov throughout the day Sunday but has gotten no replies.