More than 90% of the country’s 313 air traffic control facilities operate below the Federal Aviation Administration’s recommended staffing levels, according to an analysis of staffing data from the union representing controllers obtained by The New York Times.

As of earlier this month, 285 facilities — which include traffic control towers and other locations — were below staffing thresholds set by the FAA and the union. At 73 of those facilities, staffing is so low that at least a quarter of the workforce is missing.

The U.S. air travel system remains among the safest in the world. But persistent staff shortages and a underinvestment in safety systems have led to an alarming number of close calls between aircraft.

The shortage is particularly severe in the New York region, where two crucial facilities on Long Island are operating with nearly 40% of the positions unfilled. These facilities direct air traffic for some of the busiest airports in the United States, including Newark, JFK and LaGuardia, which handled a combined 1.2 million flights in the last year, according to data from the Port Authority of New York and New Jersey.

The FAA did not immediately respond to a request for comment.

Efforts already underway to hire and train new controllers are expected to fall short of staffing demands, according to FAA projections. Nearly three-quarters of facilities will still remain below recommended staffing levels after a long training process.

Improving the ranks may not happen quickly. It can take over four years to train a new air traffic controller at certain facilities.