The Long Island Rail Road is suspended westbound between Jamaica and Atlantic Terminal due to signal problems.
LIRR said the subways are cross-honoring.
The suspension is also causing delays on the Long Beach and Far Rockaway branches of the railroad. Service is running with delays eastbound after earlier being suspended as well.
It was the latest problem to plague the LIRR, which has been hamstrung for days by rail and signal issues compounded by the severe weather and cold temperatures.
"I have not received a level of commuter complaints like I have in the last few days, ever," state senator Todd Kaminsky said in a statement.
This is a developing story.