The elimination of weekend commuter rail service will no longer be considered an option to close the MBTA's looming budget deficit after Gov. Charlie Baker on Monday said he would "explore alternatives" to close a $42 million gap that will preserve weekend service.

Baker backed off the idea a week after transportation officials floated the possibility of saving $10 million by cutting weekend commuter rail service to and from Boston for one year while making capital upgrades to the rail lines.

The option drew criticism from Beacon Hill Democrats, and the governor appeared to gradually pull back from the concept as he first described it as part of an "options menu" that would be scrutinized by the MBTA's Fiscal Management and Control Board (FMCB), and later called service cuts a "last resort."

"Our administration is exploring alternatives to last week's MBTA budget proposals to make weekend commuter rail service more efficient, and will not pursue proposals to eliminate weekend service altogether," Baker said in a statement to the News Service Monday afternoon.

The governor was not available for an interview, but said in the statement that his administration has worked effectively with lawmakers, labor leaders and the control board to "stabilize" the T's budget and save millions of dollars that have been directed back into the system to improve service.

"I hope the FMCB continues to pursue much needed reforms, such as working with private sector experts to provide more affordable bus maintenance services, so we can invest those savings into further improving service," Baker said.

Earlier in the day at a FMCB meeting focused on another money-saving idea -- reductions to the paratransit service The Ride -- MBTA Chief Administrator Brian Shortsleeve gave little indication that the Baker administration was walking away from commuter rail service cuts.

He said there would be discussion about potential service reductions on the commuter rail next week, and also wrote a letter to lawmakers on Friday explaining that the T will already need to suspend service on commuter rail lines for work on the Green Line Extension and to complete the federally mandated positive train control -- an anti-collision safety measure.

Sen. Thomas McGee, the co-chair of the Transportation Committee, said there is a difference between eliminating weekend service and finding ways to make weekend track work and service cost effective and efficient.

"I really think it's shortsighted," McGee said. "I haven't talked to anyone who thinks getting rid of the weekend service is the way to go."

Cutting weekend commuter rail service was never going to be easy anyway, and would have likely required legislative approval to be implemented across all lines into Boston.

Facing a deficit in 2012 for the coming year's budget, then-Gov. Deval Patrick cut weekend service on the Kingston/Plymouth, Greenbush and Needham lines to fill gap. But when weekend service was restored two years later after the passage of major transportation financing law, legislators took extra steps to make it more difficult for future governors to pull back on service.

Both a 2014 transportation law and the fiscal 2015 budget included provisions ensuring the MBTA would maintain service on the Kingston/Plymouth line on Saturdays and Sunday from the Kingston/Route 3 station to South Station in Boston.

The fiscal year 2015 budget also statutorily protected Saturday service on the Needham line between Needham Heights and South Station.

MBTA spokesman Joe Pesaturo said staff had been aware of the sections "for quite some time" before it presented the budget-balancing options to the Fiscal and Management Control Board last Monday, but did not say whether board members had been made aware of the fact the legislative approval would be needed to cut weekend service on some lines.

"Last week marked the beginning of the FY18 budget process, not the end of it. There will be a robust discussion before any decisions are made, and any subsequent actions will be in compliance with Massachusetts General Laws," Pesaturo said.

McGee said cutting weekend service impacts fans traveling to the TD Garden for weekend Celtics and Bruins games, as well as health care workers commuting from outside the city to the Longwood medical area.

Recalling the 2014 provisions protecting service on certain lines, McGee said, "The thinking was the services were important services that the administration wasn't necessarily going to support." He said said he believed based on those laws that it "would probably be the case" that the Legislature would have to approve cuts on the Kingston and Needham lines.

Sen. Viriato deMacedo, a Plymouth Republican, also said he did not relish the idea of cutting rail service to his region of the state, but also said that in 2014 there was an assumption that a greater utilization of the service would reduce the size of the state subsidy to maintain the lines.

The weekday per-trip operating subsidy on the commuter rail is $5, while the weekend subsidy is $34 per trip and on some lines it exceeds $100 per trip, according to the T.

Both McGee and deMacedo said they would like to see the complete ridership numbers from the MBTA.

"I don't fault the control board for laying out all the options," deMacedo said. "I don't want to give up weekend service, but I also wasn't aware of the size of the subsidies that are still required. Is there a way to do this in a more efficient and effective manner? I think that's a fair question."

In addition to pitting Baker against Democratic lawmakers this year, the idea of commuter rail service cuts had the potential to spill over into the governor's likely re-election campaign in 2018.

Massachusetts Democratic Party Chairman Gus Bickford on Monday called on Baker to retract the "outrageous proposals" to eliminate weekend commuter rail service and RIDE service for disabled passengers.

And Democrat candidate for governor Jay Gonzalez last week called on Baker to reverse course on commuter rail service cuts and suggested weekend service could be paid for by taking back $66 million in contract add-ons approved for rail service provider Keolis.

"I think it's wrong to be cutting service that people are depending on to get to work," Gonzalez told WBZ-AM's "Nightside" program on Wednesday. "It's not OK. And this is on top of jacking up fares on riders much more than was originally planned, cutting service, particularly in underserved areas that he's already been doing, and outsourcing jobs. So we're going the wrong direction."

Gonzalez said he's been hearing complaints about the MBTA since he launched his run for governor Jan. 30.

"I've been going around the state since I started this campaign a month and a half ago and talking with lots of people across the state and in the Greater Boston area and there isn't a single person I've talked to who doesn't think service at the T has been worse over the last couple of years," he said.

Presented with Gonzalez' criticism, Baker's office last week deferred to the Massachusetts Republican Party to respond.

"Despite his best attempts to create distance from his failed record managing state finances - the fiscal woes that have plagued the MBTA land directly on Mr. Gonzalez's doorstep," party spokesman Terry MacCormack said in a statement. "Now that the Baker Administration has put the T on stable fiscal footing, the agency is making important investments in core services and improving reliability for riders for the first time in years."

For the last three years, Gonzalez' job in the insurance industry was based in Waltham, where a campaign aide said he didn't have public transportation options. For eight years when he was a partner at a downtown law firm, Gonzalez took the train or bus to work from Brookline every day, the aide said.

Michael P. Norton contributed reporting