Fifteen of the LIRR's 140 regular rush-hour trains were canceled after the rail malfunctioned about 7:40 a.m., according to an MTA spokesman.
Amtrak, which operates the tunnel along with three others in the East River, hoped to have the track operating normally by the afternoon rush hour, a spokesman said.
It was not immediately clear what caused the malfunction, the Amtrak spokesman said.
Straphangers took to social media to vent their frustration.
"Another day another delay. Possible to go thru entire week without incurring major delays? #epicfail," Bryan Wiener tweeted.
Other commuters in East Harlem and the South Bronx were also facing delays Monday morning when a water main break prompted the MTA to suspend 6 train service in the area.