Federal rail officials ordered emergency safety changes at Metro-North on Friday that would prevent engineers from speeding — and avoid derailments like the one that killed four in The Bronx.

Operator William Rockefeller was going 82 mph in a 30 mph zone when he nodded off and the train jumped the tracks.

The Federal Railroad Administration issued an order requiring that the railroad change its signal system so that an engineer would be alerted when the speed limit changes by 20 mph or more.

Currently, Metro-North’s signal system only indicates when a train is approaching a stop signal or if there is traffic ahead.

The order also mandates that a second crew member accompany the engineer in or near the train’s control compartment until the MTA implements the new changes.

The additional crew member must know the route’s physical characteristics, signal systems and be able to use the train’s emergency brakes.

“Safety is our highest priority, and we must do everything we can to learn from this tragic crash and help prevent future derailments,” said US Transportation Secretary Anthony Foxx.

Metro-North also has to give the FRA a list of locations where speed limits drop by 20 mph or more by Dec. 10, as well as an action plan for how the railroad will protect passengers’ and workers’ safety by the end of the month.

The emergency order follows a letter from the FRA on Tuesday calling on the railroad to hold safety meetings, called “stand-downs,” with workers, as well as implement a system for employees to confidentially report safety issues.

MTA Chairman Thomas Prendergast wrote in a response to the FRA on Friday that the authority would follow the order.

He said the authority is taking steps to avoid a repeat of Sunday’s tragedy.

He also said safety stand-downs had begun at the Metro-North and the Long Island Rail Road.

Almost 10,000 Metro-North and LIRR workers have done stand-downs so far. Transit workers, as well as those working at the bridges and tunnels, will hold stand-downs next week, even though they are not regulated by the FRA.

The National Transportation Safety Board is leading the investigation into the derailment, but the FRA is conducting its own probe of recent MTA incidents.

They include a May 17 train derailment in Bridgeport, Conn., that injured 50, and the May 28 death of a track worker in West Haven, Conn.

A freight train also derailed near the Spuyten Duyvil station in July, near from Sunday’s tragedy.

Gov. Cuomo sent a letter to Prendergast Friday calling on the MTA to speed up installing “positive train control” on vulnerable areas of track on the Metro-North and LIRR.

The safety system, ordered by Congress with a 2015 deadline, can reduce a train’s speed by computer in emergency situations.

He also asked for stand-downs to be held regularly.