Pilots for WA-based Qantas subsidiary Network Aviation on Thursday informed the carrier they would stop work for 24 hours on Wednesday.
The decision, relayed by the Australian Federation of Air Pilots, is the worst-case scenario for Qantas after the pilots earlier voted to take industrial action as they negotiate an enterprise agreement.
Network Aviation, which is wholly owned by Qantas, is WA's premier charter company for the mining industry.
It also employs local pilots for the carrier's regional arm QantasLink.
It was expected Wednesday's strike would disrupt at least 50 flights including charter and QantasLink flights, potentially disrupting mining operations and stranding regional passengers travelling to and from WA.
More than 85 per cent of Network Aviation's pilots, a total of 211, are members of the pilots federation.
All but one voted in favour of taking protected industrial action.
"The Australian Federation of Air Pilots remains committed to reaching an agreement for our members in Western Australia who fly for Qantas subsidiary Network Aviation and is disappointed that we have had to take this action," union senior industrial officer Chris Aikens said in a statement.
Network Aviation also flies private charters and emergency freight to and from WA, and operates more than 300 flights a week.
A QantasLink spokeswoman said the carrier had contingency plans to minimise disruption to customers if the union went ahead with the industrial action.
However, it was working to prevent the strike.
"Our proposed agreement offers our pilots significant pay rises and more guaranteed days off each roster period and we're disappointed the Australian Federation of Air Pilots has chosen to move towards industrial action while we have been trying to negotiate," the QantasLink spokeswoman said.
The enterprise agreement covers about 250 pilots who fly in WA and into Darwin.
Qantas has reached an in-principle agreement with other Network Aviation pilots represented by the Transport Workers Union and the Australian and International Pilots Association.
The carrier plans to put a proposed agreement to all Network Aviation pilots later this month including pay increases of between 13 and 20 per cent from mid-October, back-pay and three per cent annual pay increases.
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