The Federal Aviation Administration has warned Southwest Airlines and its mechanics union that their legal dispute could end up damaging the safety of the airline.

In a letter sent to the airline and the union on Friday, the agency’s top safety official, Ali Bahrami, said the dispute “raises concern about the ongoing effectiveness of the airline’s safety management system.”

Southwest sued the union on Feb. 28, claiming that a work slowdown had illegally grounded many of the airline’s planes and caused over 100 flight cancellations since the middle of the month. The lawsuit’s implication was that the union had grounded the planes to gain leverage in contract negotiations, which have been going on for years and had recently broken down over how much of the airline’s maintenance work would be outsourced.

The union, the Aircraft Mechanics Fraternal Association, said it had grounded the planes because of safety concerns.