Some of the F-16 aircraft at March Reserve Air Force Base are tasked with the Homeland Security mission of regional air defense.
The pilot was ejected and being medically evaluated.
The pilot, the only occupant on the plane, was able to eject before the crash, and was being checked by medical personnel, according to the Riverside County Sheriff in a Twitter post. According to the pilot of the helicopter, the building is used by See Water Inc.
There were five reported injuries on the ground, the U.S. Air Force Reserve said in a statement.
The crash happened at about 15:45 local time (23:45 GMT) outside the March Air Reserve Base in Perris. Herrera said there were no major injuries.
Dashcam footage shows the jet dropping towards the warehouse.
A photo from inside the building showed the wreckage buried in twisted metal and debris.
Pictures from the scene show a huge hole in the roof of the building.
The crash started a small fire that was quickly doused by the building's sprinklers, Herrera said.
'The pilot was having hydraulic problems, ' Holliday said.
A piece of the plane's canopy and a parachute were seen on the nearby runway after the pilot ejected, surviving the crash.
Damage to the warehouse was relatively minor, and there was no major fire, which Mr Holliday said was "a miracle".
The sprawling installation, located in Riverside County, California, about 65 miles (105 km) east of Los Angeles, is home to the Air Force Reserve 452nd Air Mobility Wing. Although the California Air National Guard 144th Fighter Wing, which is based in Fresno, has supported the mission there in the past, the in recent years, F-16s from out of state Air Guard units have provided aircraft and crews for the mission.