Service was suspended in both directions between Jamaica and Penn Station and also on the Port Washington branch between Woodside and Penn Station just after 10 a.m.
Eastbound service had been restored between Penn Station and Jamaica, with the first eastbound train departing Penn Station at 12:05 p.m.
Westbound service resumed shortly after with a 12:13 train from Jamaica.
The signal problems originated east of the East River tunnels.
