The union representing Qantas pilots has lodged a submission to the workplace umpire outlining its case for a new pay agreement with the airline.

Members of the Australian and International Pilots Association (AIPA) had until close of business today to deliver their paperwork to Fair Work Australia after the airline made its submission just before Christmas.

So far neither the pilots nor Qantas have revealed details of their submissions.

Both parties will take part in negotiations before an arbitration hearing at Fair Work Australia in June.

In November, Qantas and three unions -- AIPA, the Transport Workers' Union (TWU) and the Australian Licensed Aircraft Engineers' Association (ALAEA) -- were ordered to binding arbitration after they failed to resolve their bitter industrial disputes within the deadline set by Fair Work Australia.

Qantas reached a truce with ALAEA members in December, submitting a proposal to the workplace umpire that included a 3 per cent pay rise and retirement transition arrangements.

Meanwhile, AIPA says it is still pursuing a Federal Court challenge to Fair Work's ban on industrial action by all parties involved in the dispute, which it issued after Qantas grounded its fleet in October last year.

Pilots say their actions prior to the grounding were not disruptive, and included using the public address system to tell passengers their side of the story and wearing red ties.

The dispute between Qantas and its long-haul pilots centres on pay, conditions and job security.

The Federal Court is due to hear that case in February.