The operator of the Gatwick Express train service is taking the Aslef union to the high court after its drivers refused to carry passengers on new longer trains.

Govia Thameslink Railway has launched legal action over what it described as the “baffling” refusal of drivers to run the 12-carriage trains without guards.

Aslef says GTR has breached an agreement concerning driver-only trains, which it accepts on trains of up to 10 carriages. Aslef and the RMT have raised concerns over the safe operation of longer trains without guards.

Gatwick Express services had previously operated with either five or 10 carriages, but this will rise to eight or 12 across the fleet in coming months.

The dispute threatens to overshadow the introduction of the new trains, which GTR says should increase capacity as well as providing wider doors, Wi-Fi, greater reliability and comfort.

Half the services are planned to be running with 12 cars by June, but drivers refused to operate the first two planned 12-car trains without a guard. On the first occasion, the driver went to Gatwick and returned to Victoria with an empty train, although Aslef said the decision was taken by management and that the driver had offered to carry passengers if four cars were decoupled.

A GTR spokesman said: “We launch legal action very reluctantly, but we have been left with no choice because of the position adopted by the Aslef union.

“Drivers have safely operated the doors on Gatwick Express services for many years, so passengers will find their refusal to drive the new trains baffling.

“We will take any reasonable steps we can to defend the interests of our customers and maintain the Gatwick Express service with the new 12-car trains, which will increase capacity and reliability, and give a more comfortable travelling environment for passengers.”

The operator’s application for an injunction is expected to be considered at a hearing in London later this week.

An Aslef spokesman said the union believed that it had a strong case to defend, alleging that GTR was breaching agreements on train staffing. “The agreements are in place to only have 10-car coaches as driver-only, and to stop any extension of driver-only operation,” the spokesman said.

“Longer trains without guards are not safe for passengers, especially with the rise in sexual assaults, and not safe for drivers. This is purely greed and a cost-cutting measure risking safety – no member of the public has ever demanded a train without guards.”

The action is unusual for a train company, but a more confrontational attitude has been apparent in recent months after Peter Wilkinson, a senior official at the Department for Transport, told a public meeting that “we’re going to be having punch-ups” with drivers.