HAVERHILL — A high-ranking manager of the Merrimack Valley Regional Transit Authority has been charged with stealing a "significant amount of money" from bus fares.

John Whittaker, 47, of 18 Allen St., Methuen, manager of operations at the MVRTA, which operates public buses in the region, pleaded not guilty to larceny over $250 in Haverhill District Court yesterday. Judge Patricia Dowling ordered him held at Middleton jail on $5,000 cash bail.

Whittaker, who has worked for the MVRTA for 24 years, according to his attorney Joseph Gannon, was arrested at his place of employment following an investigation by state police.

Assistant Attorney General Christopher Kelly said the investigation "is ongoing." Asked after the arraignment how much money was taken, Kelly said he could not answer that question.

Harry Pierre, spokesman for Attorney General Martha Coakley, said Whittaker stole a "significant amount of money."

According to a report filed by Trooper John MacDonald of the state police, there were discrepancies of nearly $8,000 between what was actually in the MVRTA vault and what should have been there based on a computerized audit system. The discrepancies happened between Nov. 5 and Dec. 9, 2009, the report said.

State police then installed a digital camera in the cash room at the MVRTA maintenance building, 85 Railroad Ave. MacDonald said in the report that the video for May 4 shows Whittaker taking money from a vault and stuffing it into his pocket.

The discrepancies were reported to the Attorney General's Office by "a witness employed by the authority," according to MacDonald's report.

State police arrested Whittaker yesterday afternoon and brought him to Haverhill District Court. Kelly said Whittaker "admitted that he had been stealing money from the MVRTA."

Kelly asked for $10,000 cash bail because of the "seriousness of the offense" and the violation of public trust. Gannon, noting Whittaker has no history of drug or alcohol abuse and has worked for the MVRTA for 24 years, asked that he be freed on his own recognizance.

At Kelly's request, Dowling ordered Whittaker to have no contact with MVRTA employees. The judge asked Gannon to tell Whittaker "how serious the order is."

Dowling continued the case until July 8 for a pretrial conference.

"We allege that over a period of several months, Mr. Whittaker abused his position of authority to steal money from the MVRTA, resulting in a significant loss of public money," Coakley said in a prepared statement.

Bus drivers collect fares using onboard collection systems that are emptied at the MVRTA offices at the end of each day into a vault in the money room. The fares are then counted and compared to the onboard collection system readouts and subsequently deposited.

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