The Nassau County Police Department exceeded its overtime budget by $96 million over a six-year period ending in 2014, according to an audit released Monday by the county comptroller.

Police overtime from 2009 to 2014 totaled $315.2 million, which was 44 percent higher than the $218.9 million budgeted and the result of budgeting issues, inadequate record keeping, shortfalls in anticipated savings measures and complex union rules, according to the audit by Comptroller George Maragos.

Acting Police Commissioner Thomas Krumpter called Maragos’ audit a “total failure” and a “personal attack” on the police department.

Krumpter said it ignored issues such as a workforce reduction of about 500 officers in the same time period, which he said saves the county about $140 million annually and contractual obligations such as minimum-staffing mandates.

“Based on the audit, one can only conclude that the comptroller is either incompetent, biased or has a political agenda,” Krumpter said in an 18-page response in which he also called Maragos “unethical.”

Maragos denied any bias and said many of Krumpter’s assertions were “irrelevant” and his comments “disappointing.”

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“This discussion should be on the facts and we should all be focused on making the department more efficient . . . not personal insults, that doesn’t serve the public,” Maragos said.

Maragos said in an interview, the police department needs “a better management structure in place with better tools for the precincts to coordinate and schedule overtime with feedback to senior officers.”

The audit recommends the department consolidate and update minimum-staffing requirements into one document distributed to all commanding officers, develop a standard computer roll call format, and hire an outside consultant to perform a cost-benefit analysis on current workforce rules.

Krumpter said the comptroller’s audit demonstrated a lack of understanding of police operations and ignored information provided by his department.

For example, Krumpter said, one of the recommendations made in the audit called for the department to develop a standard computerized roll call format across all commands. But Krumpter said the department has already started rolling out that system and told that to the auditors but it was not included.

“He wanted to write a sensationalist report,” Krumpter said. “You can manage overtime or you can manage head count. The comptroller totally failed to recognize that work rules in this department drives overtime; we have no choice. This entire audit was about him grabbing a headline.”

County Executive Edward Mangano said he hadn’t yet reviewed the report, but he was comfortable with the level of police overtime spending.

“I would ask the comptroller to take another look at the police commissioner’s facts that he’s presenting here, so the people of Nassau County have a full understanding of what the costs are associated with the police and what the savings are.”

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Legis. Laura Curran (D-Baldwin), ranking member of the Public Safety Committee, in a statement called it “unfortunate” that Maragos and Krumpter are “at odds” and blamed the overtime increases on police precinct consolidation, that trimmed the precincts from 8 to 5.

“Yes, consolidation won savings from decreased head count, but failed to deliver on the promise that there would be no impact on police operations,” Curran said. “With better management controls and new hires, it is reasonable to expect and demand that overtime expense decrease.”

Krumpter also said two of the auditors on Maragos’ staff participated with him in “adversarial” contract talks for the Civil Service Employees Association and therefore shouldn’t have done the audit. The CSEA represents the police department’s 911 operators.

CSEA president Jerry Laricchiuta said the two Maragos staffers were not involved in negotiations.

“I think it’s irresponsible and shows bad judgment by an acting commissioner because we’re not adversarial by virtue of negotiating,” Laricchiuta said.