Of all the city programs that have ever gone wrong in New York, few could compare to CityTime, an automated system meant to streamline employee timekeeping.

Mayor Michael R. Bloomberg has called the project a “disaster,” and perhaps with good reason: the project’s cost has exceeded $600 million, nearly 10 times over budget, and is six months past its due date. Meanwhile, consultants who were hired to oversee putting the project into effect have been paid nearly $50 million  $46 million more than they were initially supposed to receive.

And on Wednesday, federal prosecutors in Manhattan charged several of the consultants with an $80 million fraud scheme that began in 2005, accusing them of manipulating the city into paying out expensive contracts to businesses that they controlled, and then redirecting some of that money to enrich themselves. They even submitted false time sheets, the authorities said.

“The issue is that here we had somebody that we trusted, or one of our contractors trusted, and that trust was misplaced,” Mr. Bloomberg told reporters. “And we just have no tolerance for this whatsoever.”