Federal agents and sheriff's deputies stormed the cockpit of a Delta Airlines flight from Minneapolis to San Francisco over the weekend and arrested the co-pilot on child sexual assault charges, authorities said.

Flight 2809 had just arrived at San Francisco International Airport at about 9:35 p.m. Saturday when agents from Homeland Security Investigations and Contra Costa County Sheriff's deputies boarded the Boeing 757-300 jet and removed the co-pilot, identified as 34-year-old Rustom Bhagwagar of Florida, the Sheriff's Office said Monday.

The investigation began in April after the Sheriff's Office received a report of sex crimes against a child, the office said. Detectives later learned that Bhagwagar was an airline pilot and was due to fly into SFO on Saturday evening. 

A spokesperson for the Department of Homeland Security told CBS News Bay Area that HSI agents assisted the sheriff's deputies by getting them airport and plane access. 

Delta Airlines told CBS News that it would defer comment to the Contra Costa County District Attorney's Office and Sheriff's Office.

"Delta has zero tolerance for unlawful conduct and will fully cooperate with law enforcement, a spokesperson said. "We are appalled by reports of the charges related to the arrest and the individual in question has been suspended pending an investigation."

A passenger aboard the flight told CBS News Bay Area that the plane had just arrived at the gate when deputies and federal agents apparently boarded through the door between the coach and first-class sections, pushing their way past passengers who were in the aisle retrieving their belongings from the overhead bins.

"These 7 people stormed the cockpit, cuffed the copilot, arrested him, walked him down the aisle, and ushered him off the plane through the cabin doors located between first and coach," said an email from the passenger, Sarah, who chose not to use her last name. "Then another set of 3 agents came up through the aisle to the cockpit and removed the copilot's luggage and personal effects.

Sarah said the remaining pilot and the flight crew appeared stunned and said they didn't know what was happening.

"It was shocking and unnerving," she added.

Bhagwagar faces five counts of sexual assault involving a child under 10 years of age and was being held at the Martinez Detention Facility on $5 million bail, the Sheriff's Office said. 

Anyone with any information about the case was asked to contact the Contra Costa County Sheriff's Investigation Division at (925) 313-2600. Tips can be sent anonymously to tips@so.cccounty.us or by calling (866) 846-3592.