A federal judge in Manhattan on Monday sentenced three men to 20 years in prison for their roles in the scandal-ridden payroll modernization project known as CityTime, and he also sharply criticized New York City’s contracting procedures for what he called a lack of “adequate and effective oversight.”

The sentences fell far short of what federal prosecutors originally sought, but they were substantially more than others imposed in public corruption cases in the city and state.

Originally budgeted to cost the city $63 million, the project skyrocketed in cost to $700 million by 2011, a federal indictment charged. Almost all of the more than $600 million that the city paid to its prime contractor, Science Applications International Corporation, “was tainted, directly or indirectly, by fraud,” the indictment said.

“It’s the largest city corruption scandal in decades,” the judge, George B. Daniels of Federal District Court, said. “It is unparalleled in its amounts, duration and sophistication.” He added, “It is a classic tale of greed and corruption.”