BOSTON (CBS) — Beverly Scott is resigning as MBTA general manager, the transportation agency said Wednesday afternoon.

The MBTA had suspended rail service Monday night and Tuesday to clear snow from its tracks amid a record-setting period of snowfall in the Boston area. Gov. Charlie Baker and others had criticized the MBTA for its lackluster performance during the extreme snow and cold.

READ: Beverly Scott’s Letter Of Resignation

Scott said in a letter that her resignation will take effect on April 11.

“Please consider this my letter of resignation as the MBTA General Manager and Rail & Transit Administrator, effective April 11, 2015,” she wrote. “Thank you and the entire MassDOT Board for your confidence and support.”

In a press conference on Tuesday, a defiant Scott blamed poor funding and aging infrastructure for the MBTA’s problems. When asked Tuesday if she would resign, Scott said “I’m not even getting into these conversations” and said she hadn’t been in direct contact with Baker.

Governor Baker was surprised when he learned Scott was stepping down.

“The Governor and Lt. Governor were surprised to learn of Dr. Scott’s resignation this afternoon,” spokesman Tim Buckley said in a statement. “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. 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.”

Boston Mayor Marty Walsh thanked Scott for her deep commitment to the MBTA, the city of Boston and the Commonwealth. “She has shown leadership and courage during the challenges we are facing, and I wish her the best of luck in the future,” Walsh said in a statement. “I look forward to working with the Governor to improve our public transportation system to better serve our residents who rely on it everyday.”

WATCH: Beverly Scott Defends Decision To Shut Down MBTA At Tuesday Press Conference

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

At a MassDOT meeting earlier on Wednesday, Scott received a unanimous vote of confidence from the MassDOT board. A MassDOT spokesman told WBZ NewsRadio 1030’s Bernice Corpuz that she handed in her resignation letter right after the meeting.

Baker’s transportation secretary Stephanie Pollack said at the meeting that the administration had “no plans” and no desire to change leadership at the MBTA.

John Jenkins, chairman of the MassDOT Board of Directors, said the search for a new general manager will begin in the coming weeks.

“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,” he said in a statement. “We hoped and expected that she would fulfill her three year contract, which ends in December of this year. I want to thank Dr. Scott for her skillful and committed leadership over the last 26 months, and wish her the very best as she moves on to her next challenge.”

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