The system, called automatic train control (ATC), is already in use on southbound trains near the derailment site.
"These are just initial steps, but we believe they will immediately improve safety for passengers on the Northeast Corridor," FRA acting Administrator Sarah Feinberg said in a news release.
Amtrak said in a statement it would implement the FRA's directives immediately.
Feinberg added that the most important safety step will be full implementation of positive train control, a more robust system for avoiding accidents than ATC.
Robert Sumwalt, a member of the National Transportation Safety Board, the agency conducting the federal probe, said this week positive train control would have prevented the accident if it was in operation along that stretch of track.
Under current law, the rail industry must adopt the technology by the end of this year.
The ill-fated train was barreling north at more than twice the 50-mile-per-hour speed limit when it entered a sharp curve and derailed, leaving a trail of tangled metal and human carnage alongside the track.
ATC detects when a train is traveling above the speed limit, sending a signal to the engineer. If the operator fails to act, the system will automatically apply the brakes.
The FRA's order came as the Southeastern Pennsylvania Transportation Authority (SEPTA) confirmed that an unidentified projectile hit one of its commuter trains operating near the derailment site about 20 to 30 minutes before the crash.
In a fresh twist to the investigation, Sumwalt revealed on Friday that the Amtrak train and a SEPTA train may have been hit by objects shortly before the accident. The NTSB has called in the FBI to examine a remnant of the locomotive's shattered windshield.
Before the disclosures, the federal probe was focusing on why the train accelerated from 70 to 106 mph in the minute before it derailed. The NTSB has not ruled out mechanical issues, human error or a deliberate act by the engineer, among other factors.