The 14-year-old veteran is facing multiple felony charges of possessing stolen sports car engines.
Green could spend more than five years in prison.
Besides possession of stolen engines, he's also charged with receiving stolen property and operating a chop shop, a term used to describe a place where stolen vehicles are taken apart and the parts then sold.
The engines are said to be worth about $15,000 each.
Investigators from a special multi-agency task force said Green stored the engines in a San Jose garage and was selling them on Craigslist.
The District Attorney's Office says the engines were taken from cars stolen all over the Bay Area over the past two years.
The Santa Clara Police Chief Mike Sellers released a statement saying in part: "This is not a true reflection of the hard-working men and women of this department that serve and protect our community."
Santa Clara has a small police force with a troubled history.
Sgt. Thomas Leipelt is on trial right now for indecent exposure following an incident last May at a store in San Jose's Santana Row in which he allegedly exposed himself to a store employee.
One day after that incident, Santa Clara Officer Kiet Nguyen was arrested for allegedly shoplifting a watch from a Target store at Westgate Center in San Jose.
Perhaps the department's most high profile problem was in 2010 when Officer Clay Rojas was arrested on felony conspiracy charges, accused of giving confidential information to a member of the Hell's Angels.
The break that led to Green's arrest on Friday came from a potential customer who thought a Chevy Camaro engine might be stolen and alerted law enforcement.
Sellers says Officer Green has been put on paid administrative leave.