The Delta Airlines pilot arrested after landing his plane at a California airport has been charged with alarming child sex crimes following an extensive investigation involving the feds, authorities said.

Rustom Bhagwagar, 34, was cuffed by federal officers Saturday night onboard Delta Flight 2809 just after it touched down in San Francisco from Minneapolis.

Bhagwagar — who was serving as co-pilot on the flight — was hit with five counts of oral copulation with a child under 10 years old, the Contra Costa County Sheriff’s office announced on Monday.

A Florida resident, Bhagwagar has been under investigation since April when the California sheriff’s office received a report about child sex crimes.

His arrest shocked passengers and flight crew alike, who were preparing to deplane when about 10 Sheriff’s office detectives and federal agents from Homeland Security Investigations (HSI) swarmed the plane and hauled the co-pilot away in handcuffs.

“A group of people with badges, guns, and different agency vests/markings were pushing their way up through the aisle to the cockpit,” one passenger who witnessed the arrest told the San Francisco Chronicle.

Another group of officers then boarded and removed Bhagwagar’s bags, and the flight’s other pilot told passengers he had “no idea what just happened” to his colleague.

Some on board the flight initially thought the arrest had to do with Bhagwagar’s immigration status – as HSI has helped lead President Trump’s migrant crackdown.

HSI told The Post it was merely helping the local police execute their arrest warrant.

“This is an ongoing local investigation with the Contra Costa County Sheriff’s Office,” a spokesperson for the agency said.

Delta has not commented on the arrest of Bhagwagar, who remains held in lieu of $5 million bail.

This is a developing story. Please check back for more information.