The Federal Transit Administration on Monday sent the railroad the bill, saying interest and penalty charges will be added.
The Record newspaper reported the FTA also said it would launch a "complete audit'' of the Access to the Region's Core project to determine how much federal funds still have not been spent.
The $8.7 billion project to construct a rail tunnel between New Jersey and New York was 15 years in the making when Christie pulled the plug, citing cost overruns.
The previous tunnel would have been America's largest public works project, creating 6,000 construction jobs at a time U.S. employment is 9.6 percent.
Officials aren't saying where NJ Transit will get the money to pay the bill.
Meantime, on Monday, Amtrak said it was in preliminary talks with New Jersey's public transit agency to study new options for building a passenger rail tunnel between Manhattan and New Jersey.
"We have been talking with them ever since the (previous) program was put in jeopardy," Cliff Cole, a spokesman for the U.S. national passenger railroad, told Reuters.