Officer Tyler Brown's police cruiser was hit at 3:40 a.m. at East Main Street and Butler Avenue, Lt. Taft Tracy said.
Emergency Medical Service units had to use the Jaws of Life to remove Cody Olachea, a 25-year-old Farmington man, and his passenger, Deseree Trujillo, a 21-year-old Aztec woman, from their vehicle.
All three were taken to San Juan Regional Medical Center.
Brown and Olachea were treated for minor injuries. Trujillo was in critical condition at the hospital on Wednesday morning. Her condition was upgraded to serious Wednesday afternoon, hospital spokeswoman Kathryn Pettijohn said.
Olachea was arrested on suspicion of DWI, Tracy said.
Tracy said Brown, who has worked as a Farmington police officer for three years and was on duty at the time of the crash, suffered a laceration to his head and is not likely to miss work because of the crash.
Brown, who reported the incident immediately after the crash, was traveling west on Main when he drove through a green light at Butler, said Beth Utley, a spokeswoman for the sheriff's office.
Olachea, driving north, ran a red light and Brown struck Olachea's two-door car on the passenger side. The collision caused significant damage to both vehicles.
Utley said Olachea showed signs of impairment and there was a bottle of vodka in the car. He was charged with great bodily harm by motor vehicle, a third-degree felony, possession of a controlled substance, a fourth-degree felony, and a misdemeanor traffic citation for running a red light.
Investigators suspect he was in possession of cocaine. A pending toxicology test will determine if the drug was in his system at the time of the crash, Utley said.
After he was treated and released from the hospital he was booked into San Juan County Detention Center.
Olachea was convicted in 2009 of a fourth-degree felony for possession of methamphetamine and marijuana distribution, according to a state-court website.
Farmington police turned over the crash investigation to the San Juan County Sheriff's Office because it involved a police officer.