Rex pilots have endorsed a new pay deal, ending a long and heated dispute between the national regional airline and the union.

The airline said 86 per cent of its SAAB twin-engine pilots voted in favour of a new four-year industrial agreement, which is expected to be formalised by the Fair Work Commission in the coming weeks.

“The vote follows over four years of protracted and arduous negotiations, during which the pandemic has wreaked huge economic misery on both the company and the pilot group,” Rex executive Paula Tran said in a statement.

“At the end, a fair and reasonable outcome was reached that enabled the company to rebuild itself and provide a good future for all its staff.”

Pilots took protected industrial action in June, saying they were disappointed by years of wage negotiations.

At the time, the airline had offered the twin-engine pilots a 5.1 per cent pay increase from July 1, plus catch-up payments amounting to eight per cent once the company recovered from COVID-19 travel restrictions.

The Australian Federation of Air Pilots said the pay offer was a cut of five per cent in real-terms, as it did not cover inflation over the previous four years.

During the dispute Rex’s deputy chairman John Sharp said the talks exposed the union’s “hypocrisy” because it agreed to a two per cent pay rise for QantasLink pilots in 2021 and 2022.

Rex also accused the union of sharing “malicious, misleading and deceptive” information with its members during the pay talks.

The airline, which flies to more than 50 regional destinations across Australia, expanded its fleet in August and returned to post-COVID profitability in September.

The union has been contacted for comment.