The new contract will merge the pilots of Atlas Air and Southern Air, acquired by Atlas in 2016, onto a single contract, reports London's Air Cargo News.
The often-fractious talks between the parties have been ongoing for more than five years and were eventually completed with the intervention of an arbitrator.
However, the pilots' union, the International Aviation Professionals (IAP) Teamsters Local 2750, has expressed disappointment at the contract.
The union said that members should have been able to vote on the final contract, adding that it had been 20 years since Atlas pilots last voted on an agreement. They also said that arbitration tended to favour companies over employees and that the contract offers a limited career path and compensates 'below the big boys'.
'This victory could have tremendous long-term negative impacts, especially in the areas of pilot recruitment and retention. You can't move cargo without pilots,' the union said in a series of Tweets.
'The contract we deserve should have been negotiated by pilots and voted on by pilots. It would not be this binding agreement forced on us by a third-party arbitrator.
'A union contract is about having a voice and defined career expectations. This forced contract guarantees that Atlas Air will be a place to train, not a place for a career.
'For pilots, this has been about career expectations, lifestyle and a voice on the job. In a time of a pilot shortage and record pilot resignations, we worry that Atlas Air Worldwide bosses just don't get it.'
The union also took umbrage at Atlas' use of 'joint collective bargaining agreement' in its press release about the completion of talks. 'It has a new forced binding agreement from a third-party arbitrator. Joint collective bargaining agreement makes it sound like we worked together. We didn't.'