An audit by New York City Comptroller John Liu cited “severe management flaws” in the city’s 911 emergency phone system upgrade, and said absentee management led to $1 billion in cost overruns.

But a spokesman for Mayor Michael Bloomberg disputes the audit’s findings that said the cost of the program has spiked to $2.3 billion. “The cost of the full program has not grown by $1 billion as the comptroller claims,” the spokesman said Thursday. “The current cost of the full program remains at $2.03 billion, which is as it has been since the fiscal 2010 budget cycle. It is not $2.3 billion — that number is wrong.”

According to the audit, the first of two by Liu’s office, the cost of the Emergency Communications Transformation Program, initiated in 2004 to consolidate emergency communications among fire, police, and emergency medical services, has spiked to $2.3 billion from $1.3 billion.

“Auditors found an alarming lack of decision-making by City Hall, which led to major technical missteps, the abandonment of a critical objective, and poor vendor performance,” Liu said in a statement. Other findings, according to the comptroller, show that the project lacks a quality assurance monitor, and the newly created agency to oversee ECTP is “ill-equipped for the job.”

The city originally hired Hewlett Packard as project manager. Northrop Grumman has been serving as lead since January 2011.

“Taxpayers are just tired of hearing about out-of-control projects involving expensive outside consultants,” Liu said. “This is unfortunately yet another example of massive waste and delay due to city management that was at best lackadaisical, and at worst, inept.”

Deputy mayor for operations Cas Holloway said the mayor’s office has already taken corrective steps. He cited Bloomberg’s establishment of the Office of CityWide Emergency Communications in 2010 to strengthen program governance.

“We appreciate the comptroller’s input — and after more than a year reviewing thousands of documents provided by the city, we are gratified that the audit validates the city’s management decisions,” Holloway said in a statement. “The result is the successful opening and operation of the city’s state-of-the-art 911 call center earlier this year, which is providing New Yorkers with the most comprehensive 911 system overhaul in four decades.”

Last week, the U.S. Attorney’s office in Manhattan and Science Applications International Corp. settled a fraud-related case in which the company agreed to pay the city more than $500 million as restitution in connection with the CityTime payroll-management system.

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