Federal corruption charges were announced on Thursday against two former close aides to Gov. Andrew M. Cuomo, a senior state official and six other people, in a blow to the governor’s innermost circle and a repudiation of the way his prized upstate economic development programs were managed.

The charges against the former aides, Joseph Percoco and Todd R. Howe, and the state official, Alain Kaloyeros, were the culmination of a long-running federal investigation into the Cuomo administration’s efforts to lure jobs and businesses to upstate New York’s limping economy by furnishing billions of dollars in state funds to developers from Buffalo to Albany.

In doing so, says a 79-page criminal complaint unsealed on Thursday, Mr. Percoco and Mr. Howe sought to enrich themselves through bribes, using their positions to help particular companies receive “hundreds of millions of dollars in state contracts and other official state benefits.”

The charges mark the second major inquiry of the Cuomo administration by the office of Preet Bharara, the United States attorney in Manhattan; eight months ago, after investigating Mr. Cuomo’s handling of an anticorruption panel that he had created and abruptly shut down, Mr. Bharara said there was “insufficient evidence to prove a federal crime.”