The San Bernardino County Sheriff's Department said the two law enforcement officers were being airlifted to a hospital with unknown injuries.
The shootout occurred after deputies who were searching for Christopher Dorner in the Big Bear area responded to a report of a stolen vehicle in the area about 12:20 p.m.
The people whose vehicle was stolen described the suspect as looking very similar to Dorner.
Police located the vehicle, and the suspect ran into the forest and barricaded himself inside a cabin. A short time later there was an exchange of gunfire between law enforcement and the suspect.
It's not clear which agency the two wounded agents belong to, State Fish and Wildlife Assistant Chief Dan Sforza told KCAL.
It's also believed Dorner previously committed a residential burglary of a cabin where a couple was tied up, an officer told The Associated Press.
The officer requested anonymity because the officer was not authorized to speak publicly about the ongoing investigation.
One of the people was able to get away and make a call.
The area is in the Big Bear region where a search for Dorner has been under way since his pickup truck was found there Thursday.
A KCAL-TV reporter in the Angelus Oaks area along Highway 38 reported gunfire in his vicinity. The noise of the gunbattle was broadcast by the station, and someone could be heard yelling at the reporter to get out of the area.
Road blocks were set up around Big Bear. A midafternoon news conference was planned in Los Angeles.
The shootout occurred in Seven Oaks off Highway 38, about five miles as the crow flies from where Dorner's pickup was found. A ridge with peaks topping 8,000 feet lies between the locations. By road, the two areas are about 30 miles apart.
The former Navy reservist began his run from the law on Feb. 6 after authorities connected the slayings of a former police captain's daughter and her fiance with an angry manifesto they said Dorner posted on Facebook. He vowed to bring "warfare" to Los Angeles police and their family members, which led the department to assign officers to guard more than 50 families connected to his so-called targets.
Within hours of the release of photos of the 6-foot, 270-pounder described as armed and "extremely dangerous," Dorner allegedly unsuccessfully tried to steal a boat in San Diego to flee to Mexico and then ambushed police in Riverside County, shooting three and killing one.
Jumpy officers guarding one of his targets in Torrance on Thursday shot and injured two women delivering newspapers because they mistook their pickup truck for Dorner's.
The hunt for Dorner appeared to go cold after his burned-out pickup was found later that morning in the mountains east of Los Angeles and his footprints disappeared on frozen ground.
Police found charred weapons and camping gear inside the truck, but it wasn't clear if he had fled into the San Bernardino Mountains near the resort town of Big Bear Lake or left the area.
Helicopters using heat-seeking technology searched the forest from above while scores of officers, some using bloodhounds, scoured the ground and checked hundreds of vacation cabins - many vacant this time of year - in the area. A snowstorm hindered the search and may have helped cover his tracks, though authorities were hopeful he would leave fresh footprints if hiding in the wilderness.
Dorner's beef with the department dated back at least five years, when he was fired for filing a false report accusing his training officer of kicking a mentally ill suspect. Dorner, who is black, claimed in his manifesto that he was the subject of racism by the department and fired for doing the right thing.
He said he would get even with those who wronged him in an event to reclaim his good name.
"You're going to see what a whistleblower can do when you take everything from him especially his NAME!!!" he wrote. "You have awoken a sleeping giant."
Chief Charlie Beck, who initially dismissed the allegations in Dorner's rant, said he would reopen the investigation into his firing - not to appease the ex-officer, but to restore confidence in the black community, which long had a fractured relationship with police that has improved in recent years.
One of the targets listed in the manifesto was former LAPD Capt. Randal Quan, who represented Dorner before the disciplinary board. Dorner claimed he put the interests of the department above his.
The first victims were Quan's daughter, Monica Quan, 28, a college basketball coach, and her fiance, Keith Lawrence, 27, who were shot multiple times in their car in a parking garage near their condo.
Dorner served in the Navy, earning a rifle marksman ribbon and pistol expert medal. He was assigned to a naval undersea warfare unit and various aviation training units, according to military records. He took leave from the LAPD for a six-month deployment to Bahrain in 2006 and 2007.