NJ Transit remains at risk of missing an end-of-the year deadline to install a critical rail safety system, federal authorities said Thursday.

Missing the Dec. 31 deadline could mean stiff fines for the rail agency or a shutdown of service on rails owned by Amtrak, which includes the heavily traveled Northeast Corridor and part of the route between Philadelphia and Atlantic City.

NJ Transit is one of nine railroads nationwide in danger of missing the  deadline mandated by Congress to install Positive Train Control (PTC), an automated system that can control a train's speed in case of an operator error. The system would prevent derailments like the Amtrak crash in Philadelphia in 2015 that killed eight people. Railroads have known for a decade they must install PTC. The deadline is designed to force railroads to have the system fully operational by the end of the year, but many, including NJ Transit, will likely not meet that mark.

Those that don't have the system fully in place can still avoid penalties by applying to the Federal Railroad Administration (FRA) through the end of the year for an extension to 2020, as long as they reach certain benchmarks. Those include having all equipment installed by the end of the year, obtaining all the radio spectrum needed for PTC communications, and making certain progress on employee training and service demonstration. NJ Transit is at risk of not meeting these standards, the FRA reported in a statement Thursday.

"We're continuing to work closely with the FRA, and we're pleased to report that that we've made substantial progress in the last six months," Nancy Snyder, an NJ Transit spokesperson, said in a statement. PTC installation went from being 12 percent complete to 60 percent in the past six months, she said, more progress than had been made in the prior six years.

To be on pace to qualify for an extension, the FRA reported, a railroad was required to have had 90 percent of its PTC system hardware in place as of June 30, 2018.

The FRA will send NJ Transit a letter detailing the finding that the railroad is at risk of missing the deadline.

In a hearing last week before state legislators in the Assembly and Senate transportation committees, New Jersey transportation officials said they have made substantial progress getting PTC up and running.

So far only one railroad, the freight carrier BNSF, has requested an extension, the FRA reported. NJ Transit has won some concessions already, though, including permission to install PTC on only half its cars, which will likely leave it with fewer resources to maintain reliable service. The FRA also granted permission to limit PTC testing to less than 17 miles of the Morristown Line by the end of the year.

NJ Transit provides 62 million trips a year statewide.

The FRA has sent NJ Transit a letter detailing why it is described as an at-risk railroad, a spokesman said.

The update on PTC installation Thursday is one of the quarterly reports the FRA has been issuing on the process. Overall, the country's railroads are showing improvement on PTC installation. Fifteen of the 40 passenger and freight railroads required to install PTC have 100 percent of the needed equipment, a list that includes SEPTA. An additional 12 have installed 95 percent to 99 percent of the needed equipment.

SEPTA's final stage of PTC installation involves ensuring compatibility with freight carriers CSX and Norfolk Southern on a portion of SEPTA's rails. A SEPTA spokesman said the system is expected to be fully interoperable with the freight railroads by the end of the year, and an extension will not be needed.

There are three fewer railroads nationwide at risk of meeting the Dec. 31 deadline than there were in the last quarterly update.

NJ Transit authorities have said they are making a frantic push to meet the deadline and the plan to shut down the Atlantic City Rail Line entirely from Sept. 5 through the end of the year will speed PTC installation. None of the route's 60 track miles has PTC equipment installed, nor do its 16 cars and four locomotives, NJ Transit officials have said.

NJ Transit is responsible for installing PTC in 282 locomotives and on 317 miles of track statewide, according to the FRA.

The decision to shut down the Atlantic City line, which provides just under 2,000 trips a workday, drew anger from some riders. They note that the South Jersey line is the only NJ Transit route being totally suspended. Some personnel and equipment will be reassigned to routes in the northern part of the state, which is experiencing cancellations and delays in part due to PTC installation.

In a statement Thursday, the transit agency expanded the discounts it will offer for Atlantic City Rail riders, many of them commuters, who will be forced to use other modes to travel.

A 25 percent discount has been expanded to all railroad tickets and passes, NJ Transit said, and will be honored on all buses between Camden and Philadelphia, the 417, 551, 554, and 555 NJ Transit buses, a shuttle bus operating through Camden, Pennsauken, and Camden, PATCO to Eighth Street in Philadelphia, and the RiverLine. The Atlantic City Rail Terminal also will remain open during the suspension.

The other at-risk railroads are: New Mexico Rail Runner Express, Capital Metropolitan Transportation Authority, Altamont Corridor Express, Maryland Area Regional Commuter, Trinity Railway Express, South Florida Regional Transportation Authority, Peninsula Corridor Joint Powers Board, and Central Florida Rail Corridor.