Atlas Air has secured an important arbitration ruling in its prolonged legal battle with the union that represents its pilots.

The US freighter operator’s parent group, Atlas Air Worldwide Holdings (AAWW), said in a statement that the August 26 arbitration decision “affirms that the merger provisions of the collective bargaining agreement (CBA) apply in connection with Atlas Air’s acquisition of Southern Air in April 2016.”

But a statement from the Airline Professionals Association, Teamsters Local 1224, said that the union will “pursue all remaining legal options" to avoid a contract resolved by an arbitrator.

The complex legal tussle between the pilots’ representatives and Atlas Air centred around the union’s decision not to provide a merged seniority list of pilots at Atlas Air and Southern Air.

In its statement AAWW said of the arbitration ruling: “It further affirms the company’s long-standing position that the union has been in violation of the existing CBA by refusing to follow the merger provisions for a new joint collective bargaining agreement (JCBA), and by failing to present an integrated pilot seniority list to the company.

“In a separate, but related, proceeding, the union was also found to be in violation of the Southern Air CBA for refusing to follow the merger provisions for this JCBA on behalf of the Southern Air pilots.”

The arbitrators in both cases ordered that the union proceed with contractually required negotiations for a new JCBA in connection with the merger.

William Flynn, chairman and chief executive of AAWW, said: “It is time for our hardworking crew of over 2,000 Atlas Air and Southern Air pilots to receive a new, competitive contract with enhanced pay and benefits.

“This has been our goal since we announced the Atlas-Southern merger in early 2016. The recent decisions by the arbitrators have made clear that the existing collective bargaining agreements provide the appropriate path for the merger and should have been followed.”

Flynn added: “Now, with these decisions behind us, the path forward is clear and we are positioned for real progress.”

The AAWW boss said that the union has “important responsibilities” as part of a process to provide the airline’s pilots “with the new contract they deserve”.

Despite the arbitration in favour of Atlas Air, there is likely to be continued turbulence in the company’s relationship with the pilots union.

Captain Robert Kirchner, a recently retired Atlas Air pilot and executive council chairman for Atlas Air pilots of Teamsters Local 1224, said: “Atlas Air executives will claim the amalgamation ruling as a victory, but this is a company in complete turmoil, and this ruling will do nothing to restore shareholder confidence or more importantly, pilot morale.

“Atlas Air has waged a vicious legal battle with its pilots for more than three years and squandered opportunities of reaching a reasonable agreement through direct, good-faith negotiations.

“Teamsters Local 1224 will pursue all remaining legal options to avoid a contract that is resolved by an arbitrator and that robs pilots of their right to vote on it and ratify as needed.”