Federal Transportation Department officials said Monday that some of the runway equipment must be tested before the FAA can increase the flight limits at the second busiest airport in the New York City area. The runway began to be used for departures Monday but won’t be available for arrivals until after that testing is completed early next week. Transportation Secretary Sean Duffy said that if all goes well, the runway should be certified by June 10.

Crews worked day and night to complete the $121 million construction project 13 days ahead of schedule and ease some of the problems at the airport. But Newark has also been plagued by cancellations and delays this spring because of a shortage of air traffic controllers after the FAA had technical problems that twice briefly knocked out the radar and communications at a facility in Philadelphia that directs planes in and out of the airport.

Five air traffic controllers went on 45-day trauma leaves after the first radar and communications outage at the Philadelphia facility on April 28, and another one is out on medical leave. That left the facility with only 16 certified controllers and five supervisors. Officials have said there are another 16 experienced controllers in training who should get certified sometime between now and October.

Duffy said “the problem we’re seeing with controllers — it can’t be fixed overnight. It takes time to train up on this airspace,” and Philadelphia isn’t alone — there’s a nationwide shortage of about 3,000 air traffic controllers.

The FAA limited the Newark airport to 28 arrivals and 28 departures an hour last month because of the construction and staff shortages. The agency has said that it expects to be able to bump up the number of flights per hour in Newark to 34 arrivals and 34 departures once the runway construction is done.

The controllers on trauma leave are scheduled to return around the middle of the month. But Duffy said the FAA has enough controllers now to handle the higher limit of 34 arrivals and departures per hour.

Before the air traffic control problems this spring, 38 or 39 flights typically took off and landed hourly at the Newark airport.

United Airlines CEO Scott Kirby said the fact that the FAA imposed firm limits on the Newark airport should significantly improve its reliability. Before these problems, airlines would routinely schedule several more flights per hour than the airport could handle during peak hours. That was a recipe for delays and cancellations.

“This agreement that the FAA drove with the airlines is really a turning point for Newark for long term,” Kirby said.

The airlines were already planning on the FAA increasing the limit to 34 arrivals and departures per hour, and the number they are selling for mid-June and thereafter already matches that limit, Kirby said.

To help get passengers through the airport while the number of flights were limited, United, which operates the most flights out of Newark, brought in bigger airplanes so they could keep passenger numbers up.

But because of all the headlines about problems, ticket sales are down, so Kirby said customers might get a deal on airfare if they are willing to fly out of Newark right now.

The FAA has said it will revisit the limits again in October because it hopes to have more controllers trained by then.

The government also upgraded the software at the air traffic control facility after a second radar outage on May 9. That helped prevent a repeat problem on May 11 when there was another problem with the lines carrying the radar signal down from New York.

Verizon has installed a new fiber optic line between Philadelphia and New York after the problems but that isn’t expected to go into service until July after testing is completed.

Duffy has said that similar problems to what happened in Philadelphia could happen anywhere because the nation’s air traffic control system relies on such outdated technology. So he’s trying to sell Congress on his expensive plan to overhaul the nation’s air traffic control system, even as most other federal agencies face steep cuts in the House Republican budget bill.