Amtrak spokesman Cliff Cole says the problem was in the south tube of the Hudson River rail tunnel so trains were forced to use the single track in the north tube.
Amtrak trains faced delays of up to 30 minutes.
New Jersey Transit says Northeast Corridor and North Jersey Coast Line trains were running up to an hour behind schedule.
Midtown Direct trains were operating to and from Hoboken.
No trains got stuck in the tunnel.
Fortunately, as of Friday evening, everything was back on schedule.