The New York Senate on Monday confirmed Gov. Andrew Cuomo’s nomination of Joseph Lhota as chairman and chief executive of the Metropolitan Transportation Authority, which runs New York City’s transit system.

In addition, the Senate confirmed the nominations of Thomas Madison as executive director of the New York Thruway Authority, and Gil Quiniones as president and CEO of the New York Power Authority. All confirmations were unanimous.

Lhota, a former New York City deputy mayor who succeeds Jay Walder, must negotiate a new deal with Transport Workers Union Local 100. The contract expires on Sunday, but the union’s executive board has already voted to keep its members working when its contract expires.

Rising debt and a revenue squeeze, in addition to a labor contract, are hovering concerns at the MTA, whose board last month passed its $12.7 billion budget and $24.3 billion capital plan through 2014.

“You can operate with a reasonable amount of debt, provided there is constant, day-to-day oversight. I view the budget as a living organism,” Lhota said after a recent board meeting.

The MTA’s finance committee will meet on Jan. 23 and its full board will convene two days later.

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