MBTA General Manager Beverly Scott submitted her resignation on Wednesday amid widespread service problems on the transit system in the wake of record snowfall, catching transportation officials and the Baker administration off guard just hours after the transportation board voted confidence in her leadership.

Scott, whose three-year contract expires in December, said she would step down on April 11. Until then, Scott said she will put "priority attention" on restoring T services to "normalcy" and putting together a first-draft performance improvement plan for the agency.

With the public transit system plagued by delays and closures following three major snowstorms in the span of two weeks, Gov. Charlie Baker has been critical of the MBTA's performance, but Transportation Secretary Stephanie Pollack on Wednesday said the administration had "no desire" to change leadership. Baker announced Tuesday his plans to meet with MBTA officials on Thursday.

Pollack also tried to downplay questions about the lack of direct communication between Gov. Charlie Baker and Scott over the past two weeks, stating she thought she was "helping" by acting as a conduit between the two leaders.

MassDOT Board member Robin Chase, the founder of Zipcar who was appointed to the board by former Gov. Deval Patrick, initiated a vote of confidence in Scott and "extreme thanks" to the employees at the MBTA that passed unanimously.

At a board meeting in downtown Boston, a parade of transportation and community activists voiced support for Scott's leadership, blaming poor performance on decades of underfunding for maintenance of the aging transit system.

"I am stunned by the resignation of Dr. Scott. Be clear, this Board has had no discussions at any time about her tenure as General Manager. We hoped and expected that she would fulfill her three year contract, which ends in December of this year," said John Jenkins, chairman of the Massachusetts Department of Transportation Board.

Jenkins, who at the board meeting apologized to riders for the lack of reliable service over the past two weeks, thanked Scott for her "skillful and committed leadership" and said in the coming weeks he would appoint a sub-committee to direct a nationwide search for her replacement.

Scott, in her resignation letter, did not give a reason for leaving before her contract expires.

"As I look forward to my next chapter - starting with some quality family time - I want to again thank you and the entire Board for your confidence and support," Scott wrote.

She continued, "No question, much more remains to be done to achieve the modern, and first-class public transportation system that all want and deserve. At the same time, on a personal professional note, the opportunity to be a part of the Patrick administration transportation team; and share in a small part of the transportation gains over the past several years has been more than worth the effort."

The MassDOT board of directors met Wednesday afternoon for the first time since Greater Boston has been battered by three major, multi-day snow events. Facing frustrated riders, MBTA crews have been trying to clear tracks of snow and keep signals and trains functioning properly.

After shutting down early on Monday night and all-day Tuesday, the MBTA restored rail service on Wednesday, but commuters still struggled to navigate commutes full of delays, shuttles buses and cancellations.

"I would like to make an apology to the users of our transportation system. You should expect to have a reliable transit system under all conditions, cold, snow, extreme snow or otherwise. In the last few weeks we have not been able to provide that to you for a variety of reasons, little or none of which is the commitment, dedications hard work and talent of the thousands of our transportation employees and its leadership team, headed by Dr. Beverly Scott," Jenkins said at the board meeting.

The chairman also said he looked forward to working with Baker and the Legislature to make needed investments in the MBTA, a recurring theme on Beacon Hill after multiple attempts to infuse new financial resources into the system.

"Shame on us if we just kick the can a little bit further down the road," Jenkins said.

Jenkins comments came after a multiple advocates for public transportation and greater funding for the MBTA voiced their support for Scott. The Black Ministerial Alliance also wrote a letter in support of Scott.

Calling her the "David Ortiz of public transportation," Conservation Law Foundation staff attorney Rafael Mares urged the board not to bend to public pressure and make Scott a "scapegoat" for the problems at the MBTA.

"I feel like she's been handed a Geo Metro and asked to enter a NASCAR race and is being criticized because she didn't win," Mares said.

Paul Regan, executive director of the MBTA Advisory Board, said the T's problems had nothing to do with management. "She's a national leader, and we're lucky to have her," Regan said.

Boston community organizer Mel King urged MBTA officials to cultivate a team spirit to push the T to achieve its potential.

Baker, who plans to meet with Scott and MBTA leaders Thursday to discuss the MBTA's recent performance, had no advance knowledge of Scott's decision to resign before the letter was emailed out through a spokesman.

Just hours earlier, Pollack said the administration fully intended to work with "this" leadership team to solve the problems at the T.

"I have to say that it's interesting that anyone would actually think that I would be part of an administration that would scapegoat Dr. Scott for the performance of the MBTA over the last few weeks," Pollack said. "The Baker-Polito administration has no plans, desire, or ability to change leadership at the MBTA. We recognize the incredibly hard work performed by Dr. Beverly Scott and her team under these recent unprecedented circumstances."

Baker spokesman Tim Buckley said the governor and Lt. Gov. Karyn Polito were "surprised" by Scott's resignation.

"They thank her for her contribution to the Commonwealth and are grateful for her offer of assistance as the MTBA transitions to a new General Manager," Buckley said. "The Governor looks forward to meeting with MTBA officials tomorrow, working with them to assess the issues that have plagued the agency in recent weeks and developing operational and maintenance plans moving forward."

Pollack noted that winter weather has put "unprecedented strains on our transportation infrastructure," indicating that MassDOT has used 2,000 pieces of equipment, 250,000 tons of salt and 700,000 gallons of liquid deicer to aid clean up.

Through Tuesday, the transportation department had spent $91 million of its $98.6 million budget for snow and ice, including $36.5 million of the $50 million in authorized deficit spending.

"Unless the rest of the season's storms cost no more than $7.6 million, we will be challenged to accommodate all of the resources we need to combat snow and ice at MassDOT. We are not working on plan to find other ways to pay vendors and pay them promptly once the budget is completely expended," Pollack said.

Calling the cold "as much of a challenge" as snow to the transit system, Pollack said the inability to provide normal service during the storms is a symptom of a larger problem of aging vehicles and infrastructure. Purchased new Orange and Red Line cars are not expected to start arriving until 2019.

"If Warren Buffett appeared today and wrote us a $2 billion check, we would still have no new vehicles for several years. You cannot go to Costco and buy Green Line cars or Red Line cars or Orange line cars," Pollack said. "What we are focusing on is the question of how are we going to operate the system we have until we build the system want and need. That is the thing I think always gets lost somewhere between running the system day-to-day and imagining the system of the future, which was quite honestly the objective of a lot of the planning and budget work over the last two or three years."

Scott, who arrived in Boston in December 2012 after running the Atlanta public transit agency, became a colorful character in Boston politics over the past two years, known for her folksy speaking style and penchant for hugging staff and members of the public.

Over the next 60 days, Scott said she would invite the American Public Transportation Association to help develop a peer "best practices assessment" and finalize the agency's 2016 budget proposal.

During an appearance on New England Cable News, Senate Transportation Committee Chairman Thomas McGee (D-Lynn) said the transportation system is "completely overwhelmed."

"The system has been underfunded for years," said McGee, a leader of the 2013 effort to adopt new system funding sources.

Noting the MBTA's role in propelling the economy, McGee said, "The state of Massachusetts has a transportation crisis."

Asked whether new taxes or fees are on the table for further system investments, McGee declined to say, calling for an honest discussion of the system's condition.

"We've been talking about this forever," McGee said. "My question would be, what plan is in place? What is the governor's plan to address what is a longstanding huge crisis with the resources that this agency has as well as the Department of Transportation in terms of the whole state?"

Senate Minority Leader Bruce Tarr called Scott's resignation a "real opportunity for change" at the MBTA.

"The cancellations of train, subway, and trolley services have been detrimental to riders trying to commute from home, work, appointments, and other destinations. The failures of the public transportation service are unacceptable and can't be allowed to continue," Tarr said. "We must all commit to making the changes that will bring forth a cost effective system that riders can rely on."

[Michael Norton contributed reporting]