A U.S. Border Patrol agent was charged Tuesday with harboring his father, a twice-deported illegal immigrant with a criminal record, in his house and then lying about his whereabouts to federal investigators, authorities said.

Marcos Gerardo Manzano Jr., 26, allegedly told his father that authorities were looking for him, and let him live at his residence in a working-class neighborhood of San Ysidro.

His father, Marcos Gerardo Manzano Sr., 46, was convicted of a marijuana offense in October 2006 and deported to Mexico a few months later, according to the criminal complaint filed in San Diego federal court.

Starting in September 2009, Manzano Sr. was seen regularly coming and going from his son’s home, according to the complaint. Last month, Manzano Jr. allegedly told an investigator inquiring about his father’s whereabouts that he had had no contact with him, although he admitted knowing he was a deported felon.

Manzano Jr. was arrested Monday night at the Border Patrol station in Imperial Beach. When an FBI Swat team raided Manzano Jr.’s home Tuesday morning, his father was gone. Another man in the residence, a deported illegal immigrant, was arrested.