New Jersey Transit riders faced another morning of difficult delays on Monday after a car caught fire inside the Lincoln Tunnel and a train stalled in one of the Hudson River rail tunnels.

The delays were the worst since several days of train problems last month drew attention to the rail tunnels’ deteriorating condition. This time, tunnel troubles affected both rail and bus riders, as the snarled traffic between New York and New Jersey caused delays lasting several hours.

The problems began around 7 a.m. when a westbound New Jersey Transit train became disabled in the northern tube of the tunnels, said Jennifer M. Nelson, a spokeswoman for the agency. The cause of the disruption was being investigated, she said, but it appeared to be related to New Jersey Transit’s equipment, not to a problem with the tunnels, which are owned by Amtrak.

New Jersey Transit said the disabled train had been removed from the tunnel around 9 a.m., but trains were still facing delays of up to an hour into and out of Pennsylvania Station in Manhattan.