The air services provider, which carries out services for QantasLink, said its employees should resist the pressure to industrial action that was recently voted on in a secret ballot.
The ballot allows pilots who are members of the Transport Workers Union to take industrial action - that includes 48-hour work stoppages and overtime bans - without the threat of legal action.
The pilots want conditions that were given away when they signed onto workplace agreements to be included in their collective agreement.
The conditions included training, promotion, equal pay and reasonable work hours.
National Jet chief executive Peter Nottage said it was premature to contemplate industrial action before finalising negotiations over increasing pilots' pay and conditions.
The company said it is offering a 12.4% pay rise over five years and will consider extra payments in return for productivity gains.
"As part of its negotiations, National Jet has made it clear that it will accept either a collective agreement or workplace agreement," the air services provider said.
The company outlined that union member pilots receive a base annual wage of between $77,500 for co-pilots and $130,000 for captains and earn extra allowances and entitlements.
"We have made a realistic offer that warrants consideration and negotiation before anyone needs to even think about industrial action," Nottage said.
"No one benefits from industrial action - it will disrupt our customers, by law it will cost pilots money if they are not at work and ultimately could damage the long-term future of our company and our employees."
National Jet said it employs more than 250 pilots and around 150 are in the contract passenger division.
The company said a large number of its workforce remain on current agreements or have elected to work with the company to agree to a way forward without taking part in industrial action.
TWU must give three days notice if union employees decide to go ahead with industrial action.
National Jet counts Rio Tinto, Minara Resources, Newcrest, Santos and Bristow Helicopters among its clients and transports FIFO workers in Western Australia, Queensland and the Northern Territory.
