William Flanagan, who rose to the upper echelon of Nassau’s police force before an arrest for abusing his power, is now behind bars after his 2013 public corruption conviction.

The former second deputy police commissioner surrendered Thursday morning to start serving his 60-day jail sentence, according to authorities.

Flanagan’s surrender came after the state’s highest court unanimously upheld his conviction earlier this month after years of appeals.

A Nassau jury had convicted Flanagan, 59, of conspiracy and two counts of official misconduct. The misdemeanor conviction came after the Nassau district attorney’s office charged that he abused his authority to try to quash the burglary arrest of a friend’s son.

Flanagan, who maintains his innocence, retired in 2012 after 29 years on the police force.

After his surrender at Nassau County’s jail, correction officials booked Flanagan at the East Meadow facility and transferred him to a Suffolk County jail in Riverhead.

Nassau Sheriff’s Department Capt. Michael Golio said jail officials requested the transfer, which the state approved, since Flanagan had served as a Nassau law enforcement official. He said such a request “is standard practice under such circumstances.”

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Suffolk County Sheriff Vincent DeMarco said Flanagan is being held in protective custody because of his prior police career. He will be locked alone in a cell for 23 hours a day and will get one hour of free time in the yard.

Jail officials will re-evaluate after a week or two to determine if Flanagan must remain in protective custody or can be moved, DeMarco said. That could include a possible transfer to the jail in Yaphank.

“This is the normal course of business. We have many people in there that are high-profile inmates,” DeMarco said. “We usually start them out in protective custody to evaluate what the security needs are going to be.”

Flanagan’s attorney, Bruce Barket of Garden City, said Thursday that he didn’t request that Flanagan be kept in protective custody but was “sure the jail will make sure that he’s safe.”

“We are continuing to pursue avenues in the state courts and consider our options in the federal court to reverse what we believe to be an unjust result,” Barket said of his client’s conviction.

In the meantime, Flanagan decided he would serve his jail time and “put that behind him,” and asked his defense team “not to seek any other stay” of his sentence, Barket said.

Suffolk jail officials said Flanagan was expected to spend close to 40 days in jail, taking into account his presumed good behavior, and said his scheduled release date was March 31.

Nassau District Attorney Madeline Singas said in a statement Thursday that Flanagan “brought scandal to his department and this county” and “nearly 8 years after his crime . . . is finally serving his sentence.”

Flanagan’s conviction came after a Nassau jury found he refused to press charges for theft of electronic equipment against a high school student with connections to Nassau’s police department.

The case involved the 2009 theft of more than $10,000 worth of electronics from John F. Kennedy High School in Bellmore.

Prosecutors said Flanagan was part of a trio of high-ranking police officials who played a role in trying to prevent the arrest of burglary suspect Zachary Parker, then a JFK senior, as a favor to his father, Gary Parker, a longtime donor to police causes.

Flanagan abused his authority to get police to return the electronics stolen by Parker to the school, and the elder Parker repaid the favor with steakhouse gift cards and a state-of-the-art flashlight, according to prosecutors.

Two other Nassau police officials, retired Det. Sgt. Alan Sharpe and retired Deputy Chief of Patrol John Hunter, pleaded guilty to official misconduct in the case.

In his appeal, Flanagan had argued he couldn’t be convicted of misconduct for actions he believed were discretionary for police as they investigate crimes. But the Court of Appeals in Albany disagreed, saying his actions were “a disavowal of a sworn duty by a public official.”