Boston Globe | June 20, 2012 | By Eric Moskowitz

The state Senate agreed Tuesday to tap $49 million from a little-known state surplus to help the MBTA close its deficit for the coming year, avoiding steeper fare increases and wider service cuts than those scheduled for July 1.

The plan, approved by a 26-9 vote after lengthy debate, largely falls in line with a measure approved by the House last week and appears destined to receive Governor Deval Patrick’s signature before a June 30 deadline. Passage places an exclamation point at the end of six contentious months for the MBTA, when thousands of riders flooded public hearings to protest fare hikes and service cuts.

The Senate bailout nearly closes the gap in the T’s $1.8 billion budget for the coming year, with officials saying they can cover the roughly $4 million gap remaining without seeking additional state money or imposing more rider pain.

But this one-time aid is a one-year fix, and robust discussion Tuesday served as a prelude to a larger and potentially more fractious debate about the state’s transportation funding crisis, with the possibility of new transportation-specific taxes on the horizon.

“I’m happy we’re able to get this legislation passed today, and I’m hopeful for the continued passion to be part of the discussion for all of us together’’ next year, said Senator Thomas M. McGee, a Lynn Democrat and Senate chairman on the Joint Transportation Committee. He said minor differences between the House and Senate versions should be ironed out before June 30. “We’re hoping we can get this done quickly.’’

As the House did, the Senate agreed to send the Massachusetts Bay Transportation Authority $49 million from a $51 million surplus generated by motor vehicle inspection sticker fees, directing the other $2 million to 15 regional authorities that provide limited bus service elsewhere in Massachusetts.

The measure also provides $1.5 million for those bus agencies from about $5 million remaining in the state’s highway snow-removal budget after a mild winter, allowing Patrick’s administration to use the remainder for the T.

The administration had sought to use both sources entirely for the MBTA, citing the statewide benefits from a system that provides nearly 1.4 million rides a day in New England’s economic center. But routing some money to the often-overlooked bus agencies beyond Greater Boston proved critical to winning legislative support.

Still, some lawmakers considered the package unpalatable, calling it a bailout for an undeserving T. That view, voiced by some legislators from Central and Western Massachusetts and from the Republican Party, contributed to nearly eight hours of debate and exposed tension about the extent to which the entire state should support the MBTA.

“For those of us outside the MBTA district, this is a bitter pill to swallow,’’ said Senator Michael R. Knapik, a Westfield Republican, saying he resented “snark-a-gram’’s from MBTA supporters suggesting lawmakers do not do enough for the T. He lamented that the money did not go to other causes. “We don’t have two nickels to rub together sometimes, and somehow miraculously we’ve been able to find this money [for the T].’’

From a conference in New York, Secretary of Transportation Richard A. Davey issued a statement thanking the Senate “for its continued partnership’’ and expressing a commitment “to work with our legislative partners to find a long-term solution to the challenges that face not only the MBTA, but our entire transportation system.’’

Needing to erase a $160 million deficit, MBTA leaders proposed in January to cover the gap with massive fare increases and widespread cuts. Most riders called for more service, not less, for the sake of the region’s economy, environment, and quality of life.

So the Patrick administration revised its proposal, settling on a smattering of cuts and a 30-cent bump on CharlieCard subway fares and 25-cent increases on bus fares to close most of the deficit. The T board approved the plan in April, with the administration turning to lawmakers for help with the rest.

Seniors and the disabled, who have long received significant discounts, face disproportionate increases. Users of The Ride, a service for the disabled, are seeing fares at least double. The Senate asked the T to study the effect of those changes during the next six months.

The Senate plan calls on the Patrick administration to articulate a proposal by the end of the year for sustaining the state’s transportation system, including possible new revenues, before lawmakers take up the issue again.

“Though our public transportation systems need to be subsidized, the [Department of Transportation] cannot keep coming back and asking for money,’’ Senate President Therese Murray said. “There must be a much broader conversation about [the state’s] massive transportation funding problems.’’

The T historically had little incentive for efficiency, relying on lawmakers to close the gap between its income, mostly from fares and expenses. That changed a dozen years ago, when lawmakers ordered the MBTA to balance its books and gave it 20 percent of the state’s sales tax revenue to help. In the process, they saddled the T with billions in debt to pay off politically popular but unfunded transit expansions, some of them required to offset the Big Dig highway project and comply with federal environmental law.

The change forced the T to become more efficient, wringing more money from advertising and real estate and reducing staffing levels even while expanding service; it now stacks up comparably or better with peer agencies on operating expenses per passenger and mile.

Analysts have said the Legislature’s earlier action imposed discipline on the T, but left the agency too indebted and too reliant on the sales tax, which has flagged amid recessions and a shift in consumer purchasing to out-of-state online retailers. No other major transit agency is as saddled with debt.

But some lawmakers Tuesday called the T badly mismanaged. It “is clearly a broken system in need of dire repair,’’ said Senator Gale D. Candaras, a Wilbraham Democrat, unsuccessfully seeking a control board to take over the T. “Not only is this proposed bailout with no strings attached unfair, it would be irresponsible.’’

Senator Patricia D. Jehlen, a Somerville Democrat, said “bailout’’ was a fraught term that might apply to failed banks but not public entities providing broad benefits and facing annual cost increases.

Eric Moskowitz can be reached at emoskowitz@globe.com.