WIlliam Flanagan, left, leaves a Nassau County courtroom. (Feb. 14,...

WIlliam Flanagan, left, leaves a Nassau County courtroom. (Feb. 14, 2013) Credit: Newsday/Thomas A. Ferrara

A former Nassau police commander was found guilty Thursday of two misdemeanor official misconduct charges in a case accusing him of misusing his influence to prevent the arrest of his friend's son.

The jury foreman in the trial of former Second Deputy Commissioner William Flanagan told the judge -- who had kept the panel late to deliberate -- that jurors were deadlocked on the other two charges, including the one felony charge of receiving reward for official misconduct. He said the jury couldn't reach a unanimous decision even "after many votes."

Flanagan, who could face up to a year in jail on the misdemeanor convictions, looked stoic and calm as the partial verdict was read about 7:30 p.m.

State Supreme Court Justice Mark Cohen ordered jurors to continue deliberating on the remaining charges, then released them at 9 p.m. The jury will resume its work this morning at 9:30 a.m.

After the partial verdict, Flanagan's attorney, Bruce Barket of Garden City, said Flanagan's "position throughout this case has been that he did nothing wrong. This mistaken jury verdict does not change that. We will not rest until he is exonerated."

Flanagan did not immediately comment.

A spokesman for Nassau County District Attorney Kathleen Rice said she had no immediate comment.

The jury has been deliberating since Friday morning, with a break on Tuesday, a court holiday. When one juror called in sick Wednesday, the judge replaced her with an alternate and ordered the jury to begin deliberating from scratch.

Prosecutors say Flanagan improperly used his influence to get police to return electronics equipment to John F. Kennedy High School in Bellmore in 2009 after Zachary Parker, son of police benefactor Gary Parker, stole it. Prosecutor Bernadette Ford said Gary Parker believed that returning the property would help persuade school officials not to press charges against his son.

Gary Parker repaid the favor by giving Flanagan two $100 gift cards to Morton's steak house and a state-of-the-art flashlight, Ford said in her summation.

Flanagan was charged with receiving reward for official misconduct, a class E felony, two counts of official misconduct and misdemeanor conspiracy in the sixth degree. He faces up to 4 years in prison if convicted of the felony charge.

"This time it's not what you did, but who you know or who your father knows," Ford told the jury in summations.

Zachary Parker was never arrested by police, but prosecutors later presented his case to a grand jury, which indicted him. He later pleaded guilty to burglary charges.

The controversial case has pitted Rice and some top prosecutors against some high-ranking current and former police officials, many of whom packed the courtroom during the trial. Rep. Peter King (R-Seaford) came to support Flanagan, as did former Nassau Police Commissioner Lawrence Mulvey.

Barket had argued it is not illegal for police to return stolen property to the owner, and there was no evidence that Flanagan asked anyone not to arrest Zachary Parker. The gift cards are not improper unless they are a reward for doing something wrong, he said.

With Chau Lam

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