Metro’s board of directors approved a combined operating and capital budget of $2.5 billion for fiscal 2012 on Thursday without imposing any major rail fare increases.

The transit agency had a $66 million deficit in its $1.48 billion operating budget, but Maryland, Virginia and the District closed the shortfall by making larger contributions. Metro’s management also found internal cost savings, and the agency altered some bus routes.

The largest sources of income in the operating budget for the period that begins July 1 are $663.6 million in rail revenue and a $621.9 million payment from the local jurisdictions. Bus revenue is estimated at $141.9 million. The operating budget also will:

l Increase the bus-to-rail and rail-to-bus transfer fare by 50 cents on some bus routes in Anacostia and Congress Heights.

l Eliminate a special cheaper fare for some bus riders in Anacostia.

l End the N8 and K1 bus lines, which run to Tenleytown-Glover Park and Takoma-Walter Reed, respectively.

l Create a bus route, the 7M, to run between the Pentagon and Mark Center.

“We listened to our riders, who told us not to raise fares or cut services, and requested jurisdictional commitment through increases in contributions,” Metro board chairwoman Catherine Hudgins said in a statement after the panel unanimously passed the budget.

Last year, Metro took about $30 million from its capital budget to help make up for a shortfall in its operating budget. The 2012 operating budget replaces that money.

About $2 million of the repayment will go to reconstructing escalators and the rest will go to buying 51 buses a year earlier than planned, said Metro General Manager Richard Sarles. Metro is already spending $148 million on replacing and rehabilitating some of its 588 escalators.

“The fact that we were able to get through the year with operating results that were $30 million better than expected shows me we’re managing the place well,” said Mort Downey, a federal government representative to Metro’s board.

The difference between last year’s budget process, when Metro had a $189 million shortfall, and this year’s was “night and day,” said Marcel Acosta, the other federal representative to the board.

At its Thursday meeting, the board also discussed safety issues. On Wednesday, officials marked the second anniversary of the deadliest crash in Metro’s history, which killed nine people.

Matt Bassett, head of the the Tri-State Oversight Committee, which monitors safety at Metro, told the board that Metro had made improvements to operate its rail system more safely but still has work to do — which Metro does not dispute.

Bassett said the agency has done a better job in adding supervisors to rail yards, reviewing training, improving communication between Metro’s operations control center dispatchers and track maintenance personnel, and giving the TOC better notification when incidents occur.

He cautioned, however, that “the fact that they’re reporting and analyzing rule violation incidents is great, but the fact that they’re happening at all is clearly not so great.”

On another safety issue, Sarles said Metro received 339 calls for service in the first half of the year for a “suspicious person, package, bomb threat or similar condition” but assured the board that the agency has policies in place to deal with such situations.

On Friday, Metro’s top officials are expected to testify before a House panel about the agency’s security measures. This follows a bomb scare June 13 along the Red Line at the Rockville Station.