The incident happened at approximately 11 a.m. Sunday near Otay Mesa Road and Harvest Street, when a twin-engine Sabreliner and a single-engine Cessna 172 collided, according to preliminary reports.
"It appears that it was a very violent crash, as you can tell by both aircrafts that are in multiple pieces," said Cal Fire Division Chief Nick Schuler.
Both planes were reportedly approaching Brown Field, an airport close to the U.S.-Mexico border.
The National Transportation Safety Board confirmed the Sabreliner involved in the crash was leased by military contractor BAE Systems on a mission training flight.
"BAE Systems was alerted this afternoon that a small aircraft carrying its employees collided with another," the company said in a statement to NBC7, adding that its "employees and their families are our first priority, and we are prepared to offer all our support."
Safety board investigator Andrew Swick said the pilot of the Cessna, who was also killed in the crash, was on a cross-country trip.
"We don’t know anything about the identities the victims nor where they were taking off or where they were going," Schuler said. "We don’t who the planes belong to, either."
Schuler had originally reported the death toll at 4.
The two planes crashed at different wreckage sites at least a mile apart from each other. The Sabreliner crashed on a grassy slope, and the Cessna fell within the bounds of the San Diego National Wildlife Refuge.
The wreckage ignited several nearby brush fires. Flames were quickly put out by fire crews on the ground and a helicopter dumping water on the area.
One Chula Vista firefighter was taken to the hospital after he suffered a minor heat-related exhaustion injury, Schuler said.