(KRON) — Flights resumed at Bay Area airports Wednesday morning after delays caused by a glitch in a Federal Aviation Administration computer system. Flights were grounded across the nation at 3:29 a.m. Pacific time, after a malfunction of the Notice to Air Missions System, according to a statement from the FAA.

The cause of the glitch has not yet been determined.

Departures resumed at Oakland International Airport at 6:05 a.m., according to airport spokesperson Kaley Skantz. She said the ground stop order was lifted before many flights were scheduled to depart and had a minimal impact starting at 5 a.m.

San Francisco International Airport also resumed normal operations just after 6 a.m., airport spokesperson Doug Yakel said in an email. Yakel said 83 flights were delayed as of 7:22 a.m., which is about 9 percent of all flights at SFO, a figure he said was normal for the airport. He also said there were about 20 cancellations Wednesday morning, which he also described as routine and said it was impossible to determine how many were affected by the FAA glitch compared to other factors.

Mineta San Jose International Airport resumed normal operations at about 6:30 a.m., said airport spokesman Keonnis Taylor. Taylor said just one flight was delayed due to the stoppage. Nationwide, Newark Liberty International Airport in New Jersey and Hartsfield-Jackson Atlanta International Airport in Georgia were the most impacted by the stoppage, according to the FAA’s statement.

After a NOTAM computer system failure at the Federal Aviation Administration (FAA) caused a temporary nationwide pause in flight operations, the FAA announced that normal air traffic operations have resumed at all airports across the country.

The ground stop ordered by the administration has also been lifted.

Secretary of Transportation Pete Buttigieg said on Twitter, “FAA has determined that the safety system affected by the overnight outage is fully restored, and the nationwide ground stop will be lifted effective immediately. I have directed an after-action process to determine root causes and recommend next steps.”

The administration originally ordered all airlines to pause all domestic departures until 9 a.m. ET to allow the agency to validate the integrity of flight and safety information.

However, travel journalist Peter Greenberg told NewsNation that the 9 a.m. ET estimated time of recovery is just a relative term.

He said, “The airlines will not get back on track for many hours today. You’ll see a number of delays morphed into full cancellations. Otherwise, the airlines can’t stabilize their schedules.”

As of 10 a.m. ET, over 5,400 flights have been delayed within the U.S. and nearly 900 flights have been canceled, according to FlightAware.

Greenberg said the good news for travelers affected by the pause is that it isn’t a peak travel time — in fact, it’s actually a weak travel time. This means that if travelers run into cancellations, the odds are that they may be able to get on another flight later in the day, he said.

For departing flights, the pause started a cascading ripple effect that Greenberg said could easily extend into Thursday.

The NOTAM system is responsible for communicating flight hazards and real-time restrictions to pilots, making it hazardous for pilots to take off without it.

In a fourth update, the FAA announced operations at Newark Liberty International Airport and Hartsfield-Jackson Atlanta International Airport resumed due to air traffic congestion in those areas, even though other airports were asked to continue the ground stop.

Buttigieg briefed President Joe Biden on the FAA system outage Wednesday morning, according to White House press secretary Karine Jean-Pierre.

“There is no evidence of a cyberattack at this point, but the President directed DOT to conduct a full investigation into the causes,” Jean-Pierre tweeted.

The cause of the outage is still undetermined, but Greenberg said this was the first time he’s seen a ground stop since the historical events on Sept. 11, 2001.

“Aircraft can still land safely, just not take off right now. They don’t know what the cause of it is, they expect in a couple of hours they’ll have a good sense of what caused it and will respond at that time,” Biden said.

The FAA supported Biden’s statement, saying that all flights in the sky during the departure pause were safe to land. The administration explained that pilots check the NOTAM system before they fly.

“A Notice to Air Missions alerts pilots about closed runways, equipment outages and other potential hazards along a flight route or at a location that could affect the flight,” the FAA tweeted.

In its original tweet, the FAA announced that it was performing final validation checks and reloading the system. It also announced that flight operations across the National Airspace System would be affected.

“The irony about it is that the FAA has been talking about next-gen for two generations, this will be a huge wake-up call to get Congress to act to perhaps possibly give them more money to get it in place sooner,” Greenberg said that the FAA has been trying to change its antiquated system for years.

The FAA said the outage meant that no flights were able to be released, and airports across the nation had reported thousands of delays.

“United has temporarily delayed all domestic flights and will issue an update when we learn more from the FAA,” United Airlines told NewsNation in an initial statement.

Once the ground stop lifted, United announced they have activated a travel waiver for any customers who need to change their plans, including offering refunds for flyers who no longer want to travel.

The U.S. Travel Association released a statement, calling for federal action in response to the outage:

“Today’s FAA catastrophic system failure is a clear sign that America’s transportation network desperately needs significant upgrades. Americans deserve an end-to-end travel experience that is seamless and secure … We call on federal policymakers to modernize our vital air travel infrastructure to ensure our systems are able to meet demand safely and efficiently.”

Bay City News contributed to this report.