SAN FRANCISCO — Two passenger planes aborted landing at San Francisco International Airport last week after pilots saw a Southwest Airlines jet taxiing on the runways where the other planes had been cleared to land.

An air traffic controller told the Southwest pilots that they should not have been on the runways during the May 19 incident.

The Federal Aviation Administration said Thursday that the Southwest plane cleared the runways when the other planes passed directly overhead, and that the decision to abort the landings was «out of an abundance of caution.»

“The FAA investigated the events and determined that appropriate steps were taken to ensure safe operations,” the agency said.

The National Transportation Safety Board said it is not investigating the matter.

The incident comes after half a dozen close calls in recent months that are being investigated by security officials. These include one in February in which a FedEx plane flew about 100 feet above a Southwest jet in Austin, Texas, after an air traffic controller cleared both planes to use the same runway.

In this month’s incident, an incoming United Airlines plane flew as low as a few hundred feet over San Francisco Bay before pilots saw the Southwest plane on the same runway and decided to abandon its landing.

Shortly after that, the crew of an incoming Alaska Airlines plane saw the same Southwest jet crossing a second parallel runway, and the pilots also aborted their landing.

Both the United and Alaskan planes turned around and landed safely.

The air traffic controller told the crew of the Southwest plane, «They shouldn’t be on the runway,» according to a recording captured by LiveATC.com. When one of the pilots tried to explain himself, the controller cut him off and said, «I don’t need an argument.»

The incident was first reported by the San Francisco Chronicle. The San Francisco airport was the scene of a terrifying near disaster in 2017when pilots of an Air Canada plane mistook a taxiway for their runway and nearly landed on top of four other planes waiting to take off.

Despite recent close calls, the acting FAA chief has said the nation’s air traffic system is safe, noting the lack of a fatal crash involving a US airline since 2009.

However, concern over close calls led the FAA to hold a «safety summit» in March. The agency said this week it is investing $100 million in improvements at 12 airports, but not in San Francisco, to reduce the number of «runway incursions», when an aircraft or airport vehicle is on a runway when it shouldn’t be.