Caltrain will keep all of its 86 weekday trains running in the next fiscal year, though riders will have to shell out a little extra for tickets and parking, the agency's board of directors decided Thursday morning.

The Peninsula Corridor Joint Powers Board, which oversees the cash-strapped transit agency, voted 5-3 Thursday morning to adopt a budget plan that depends largely on one-time revenues to balance the books in fiscal year 2012. The approved plan also assumes the agency will close its projected $3.5 million budget deficit through a contribution from the Metropolitan Transportation Commission (MTC), a regional planning agency.

Though the final details of the deal are still being negotiated, the money would likely be transferred from the Metropolitan Transportation Commission's allocation for Caltrain's capital budget to its annual operating budget, Caltrain staff said Thursday. Caltrain CEO Michael Scanlon called the deal a "one-year patch" and said the money could come from a vehicle-replacement budget, which is already underfunded.

"It's a complicated deal," Scanlon told the board. "It's close to done. There's been good, positive spirit that has characterized the talks between the partners and the MTC."

Under the plan, train fare would go up by 25 cents, while the daily parking costs would rise from $3 to $4 starting July 1. The cost of the monthly parking pass would go up from $30 to $40.

Members of the public and the board majority hailed the plan as a victory, however temporary, to the agency's ongoing budget crisis. Caltrain staff had previously proposed reducing service to 76, or possibly even 48, trains, suspending weekend service at some stations (including California Avenue in Palo Alto) and closing other stations altogether. These proposals drew heated opposition from the public, with riders, business owners and city officials packing into recent public hearings to urge the agency to keep its service levels intact.

The board agreed to adopt the staff proposal to keep all 86 trains running and to keep stations open and weekend service intact. But members also warned that most of the fixes in the proposal are only good for the next fiscal year and that the agency still faces the monumental task of getting permanent, dedicated funding.

This is the third year that the Caltrain board has declared a fiscal emergency.

"The reality is that we have to be in this together during these two years to come up with a solution because we could be back here with something far more serious than what we're talking about now," said Director Adrienne Tissier, who made the motion to accept the new budget plan.

Director Liz Kniss said she was "amazed" that the agency was able to come up with a plan this quickly and called the proposal "very satisfying." Director Ken Yeager agreed, though he acknowledged that the long-term problem is far from solved.

"I think we all sensed the message that this is a service that we'd like to maintain as much as we could," Yeager said. "Even though we got the little train up the hill this time, there's a lot of clouds."

Board Vice Chair Omar Ahmad, who along with Chair Sean Elsbernd and Director Jose Cisneros opposed the resolution, called the proposal a "one-time spending plan" that is "not a solution" to the agency's financial struggles. He proposed an amendment that, barring a new funding source, would have established a 48-weekday-train model as the "sustainable" service model for the agency. His amendment failed, with only Elsbernd and Cisneros supporting it.

"I absolutely guarantee with the budget we're about to adopt, we'll be here in January or February declaring a fiscal emergency," Elsbernd said. "The underbelly of this system is completely corroded."