Ryanair’s UK flights were operating as normal on Thursday morning despite a strike by pilots, the airline has said.

There were fears of widespread disruption after a judge rejected a high court attempt by the airline to force pilots to return to work.

Ryanair reported a 97% punctuality rate for its first departures and arrivals at UK airports on Thursday, blaming the small number of delays on air traffic control issues.

A judge rejected an application on Wednesday for an injunction against the British Airline Pilots’ Association (Balpa), which would have forced pilots to return to work.

Balpa said it had offered to reopen negotiations with the airline after the ruling, in a final attempt to avert strike action. The union said the Ireland-based airline had “rejected the offer out of hand”, so the strikes would go ahead as planned between 00:01 on Thursday until 23:59 on Friday.

Brian Strutton,the union’s general secretary, said Balpa had attempted to re-enter negotiations, claiming “we extended an olive branch to Ryanair as a way of getting back around the table and calling off strikes over the next two days”.

Balpa said the walkout was caused by a longstanding dispute over pay and conditions.

The airline said it expected most of its flights to continue as normal, emphasising that while small disruptions could occur, it it did not expect significant disruptions during the strike.

A second round of industrial action is due to take place from 2 to 4 September.