Airports across the USA have been thrown into chaos after a dramatic nationwide stop order forced the grounding of thousands of planes.

A ‘ground stop’ notice was issued across the country because of a “glitch” in the system that provides safety information to pilots before flying.

So far more than 6000 flights have been delayed and nearly 1000 cancelled according to the FlightAware website, as officials said it would take hours to recover from the halt.

On Thursday morning (AEDT), flights were slowly resuming departures as the ground stop was lifted.

But the number of flights affected rose even after the stoppage order was cancelled.

The Federal Aviation Administration (FAA) was scrambling to fix the outage which messed up the travel plans of thousands of frustrated passengers.

The affected system is known as the Notice to Air Missions.

The Biden administration said the problem did not appear to have been caused by a cyber attack, and the cause could be known in a few hours.

White House Secretary Karine Jean-Pierre said in a tweet that a full investigation would be ordered.

Tweet from @PressSec

When asked if the outage was caused by an out-of-date system, Transportation Secretary Pete Buttigieg told CNN it was one of the “key questions” that would be looked at.

Mr Buttigieg pledged a “process to determine root causes and recommend next steps”.

The drama occurred at a typically slow time after the holiday travel season but demand remains strong as travel continues to recover to near pre-pandemic levels.

The FAA tweeted that normal air traffic operations were resuming gradually across the US.

“The ground stop has been lifted. We continue to look into the cause of the initial problem.”

One issue airlines are facing is trying to get planes in and out of crowded gates, which is causing further delays.

Passengers wait for their flights at LaGuardia airport in New York. Photo: Getty

At an airport in Greenville, South Carolina, Justin Kennedy abandoned a work trip to nearby Charlotte.

He said confusion reigned as airline employees were not aware what the FAA was saying, and many passengers were initially unaware of the delays.

“I sat in a Chick-fil-A dining area that had a good view of the TSA exit,” the 30-year-old information technology employee said.

“I saw at least four people sprinting to gates because they thought they were going to miss their flight, only to come back to the food court, out of breath.”

Captain Chris Torres, vice president of the Allied Pilots Association, said the outage could affect traffic through to Friday.

“This thing was lifted at 9am Eastern. That doesn’t mean the problem stops at 9am. This is going to cause ripple effects,” said Torres, whose members fly for American Airlines.

“The end result of this is going to be very similar to big weather events.”

The FAA had earlier ordered airlines to pause all domestic departures after its pilot alerting system crashed and the agency had to perform a hard reset about 2am, officials said.

Flights already in the air were allowed to continue to their destinations.

A NOTAM is a notice containing information essential to personnel concerned with flight operations but not known far enough in advance to be publicised by other means.

A ground stop is an air traffic control measure that slows or halts aircraft at a given airport.

A total of 21,464 U.S. flights were scheduled to depart on Wednesday with a capacity of nearly 2.9 million passengers, data from Cirium showed.