An Amtrak spokesman says the signal problems are centered near Rahway. Spokesman Clifford Cole says work crews are on the scene.
Some minor delays continue, but the morning rush hour is expected to be normal.
NJ Transit had cancelled several departures from New York City on the Northeast Corridor and North Jersey Coast lines between 7 p.m. and 8 p.m. and was cross-honoring bus and train tickets on PATH trains between New York and New Jersey.
Raritan Valley Line trains were delayed up to 30 minutes.