The Fastrak work will impact service from 10 p.m. to 5 a.m. Monday through Friday next week.
Service on the F, R, M and E lines were disrupted Tuesday evening.
A small track fire broke out in the tunnel between Queensboro Plaza and 57th Street, officials said.
The trains were rerouted and service was delayed after reports of a person injured at Avenue M.
The 1, 2, 3, 4, 5, 6, 7, A, C, D, E, F, G, J, M and S lines will have changes.
A man was hit by an F train in the Fourth Avenue station Monday morning, officials said.
The 1, 2, 3, 4, 5, 6, 7, A, D, E, F, G, N and R lines are all slated to undergo service disruptions.
Crews were working to repair the rail at 59th Street, an MTA spokesman said.
Work will affect the 2, 3, 4, 5, 6, 7, A, E, F, G, J, M, Q and two shuttle lines, the MTA said.
An empty suitcase prompted 1, 2 and 3 trains to temporarily bypass Times Square Monday, police said.
The G train will undergo overnight repairs Wednesday and Thursday.
The 6 train was suspended from Hunts Point Avenue to 125th Street after a water main broke, the MTA said.
The 1 train was temporarily suspended as crews repaired damaged tracks after a derailment Wednesday.
Maintenance was set to disrupt 1, 2, 4, 5, 7, A, C, E, F, G, J, M, N, Q, and R trains over the weekend.
The Staten Island Railway will not stop at the terminal this weekend because of construction.
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