Gov. Chris Christie directed New Jersey Transit late Wednesday to halt all payments to Amtrak because of a train derailment on Monday and subsequent delays that have ensnarled Garden State commuters this week, according to two letters obtained by The New York Times.

In a letter to Anthony R. Coscia, the chairman of the Amtrak board, the governor said that he had directed New Jersey Transit “to cease making any payments to Amtrak” until there had been a “thorough and independent examination of the tracks, signals, switches and other equipment maintained by Amtrak” on the Northeast Corridor and verification that the equipment was “in a state-of-good-repair.”

As part of a longstanding agreement, New Jersey Transit pays Amtrak for its use of both the Hudson River tunnels and the Northeast Corridor rail lines, which Amtrak owns. According to the letter, New Jersey Transit pays Amtrak $2.5 million to $5 million a month for operating expenses and recently paid an additional $62 million for capital investments in the Northeast Corridor as part of the agreement. Mr. Christie is directing that these funds be withheld in future payments.