The MBTA paused nearly all of its contractor work on its tracks for 48 hours starting Wednesday as the agency manages its response to federal restrictions that were put in place because of a series of near misses between trains and employees, according to internal communications obtained by the Herald.

Deputy Chief of Engineering and Maintenance Megan Chann made the pause on all contractor work requiring track access clear in at least one internal email sent late Wednesday night to agency staff. The email came the same day a handful of near misses on the Red Line were made public and a week after federal regulators cracked down on the MBTA.

Contractor work is permitted on work orders that do not need track access and “in established diversion areas under the direction of construction and logistics,” Chann said in the email.

“The safety of all of our work crews is our top priority, so we appreciate your patience as we work through this response,” Chann wrote in the 11:30 p.m. email.

MBTA spokesman Joe Pesaturo said the agency is working to establish “more rigorous levels of protection for work crews on our rights of way.”

“The first priority is to ensure safety for our internal workforce supporting critical inspections and maintenance,” Pesaturo said in an emailed statement to the Herald. “In order to focus on this first phase of work, the MBTA has paused (for 48 hours) all contractor work that is not taking place inside an established diversion area.”

In an email Friday just before 8:30 a.m., Pesaturo said the pause started Wednesday and was scheduled to end in about 10 hours.

The pause on contractor work comes as MBTA General Manager Phillip Eng continued to push back on federal restrictions barring lone workers from accessing tracks, a scenario the Federal Transit Administration barred because of the near misses.

In a Wednesday letter to FTA Chief Safety Officer Joe DeLorenzo, Eng sought to clarify the MBTA’s “transition plan to address the immediate concerns around our most recent near misses and to respond to the [FTA’s] immediate action letter” sent on Sept. 14.

Eng said the MBTA proposed “one specific amendment to the lone worker prohibition for the FTA’s consideration.” It is not the first time Eng has pushed the feds to allow for the continued use of single employees on tracks; he argued that position in a separate letter last week.

But Wednesday’s message to DeLorenzo outlines specific scenarios in which Eng views the use of lone workers as necessary, including to deal with disabled trains, hand throw a switch for a switch flashing out of correspondence, or a dropped track circuit, among other things.

“If any one of these circumstances arises and the response to a lone worker is deemed necessary by the [operations control center] supervisor, the responding personnel must be given level one protection with positive communication and verbatim repeat-backs with vehicle operators to establish the protection,” Eng said in the letter.

A spokesperson for the FTA did not respond to a request for comment.

Eng’s letter follows the Sept. 14 letter from the FTA, which came in response to four near misses. In that letter, DeLorenzo said the FTA had “determined that a combination of unsafe conditions and practices exist such that there is a substantial risk of serious injury or death of a worker.”

Among the restrictions was the prohibition on lone workers, also known as level five protection, which the FTA said it was prohibiting “until the MBTA can demonstrate that sufficient procedures are in place to protect these workers.”

“Failure to comply with these requirements may result in suspension of all activities that place workers on the ROW, including maintenance and inspection, until FTA is confident that the MBTA can ensure workers are adequately protected from collisions on the ROW,” the letter from the feds said.

Pesaturo said the MBTA is looking to establish “more rigorous levels of protection for work crews on our rights of way.”

“Eng is rebuilding and reorganizing the workforce, top to bottom, to ensure we have the right people in place at all levels to implement the changes required to bring meaningful, long-lasting systemic solutions,” Pesaturo said in a statement. “T management is working to ensure that improved safety procedures are being implemented and that the workforce has proper guidance and support.”

The request from the MBTA to continue some use of lone workers is “completely appropriate,” said Stacy Thompson, executive director of LivableStreets.

“I unfortunately think that the FTA is following an old playbook, where they sort of just stopped work, ask agencies to send them more paperwork and don’t offer meaningful solutions,” Thompson said. “… I’m quite pleased to see the T pushing back a little bit on a somewhat heavy handed approach that is frankly not helpful at the moment.”

Other MBTA responses to the restrictions the FTA put in place because of near misses include shifting mobile tack inspections to night hours.

“MBTA will work to establish ‘maintenance diversions’ for night work to ensure no vehicles enter areas designated for on-foot work with physical barriers and a designated person in charge to supervise and coordinate appropriate safety controls,” Eng said.

Correction: A previous version of this story said the pause on nearly all contractor work started Thursday. The pause began on Wednesday.