Jetstar boss Alan Joyce has blasted the Qantas pilots union's "lunatic" assault on his airline, accusing the Australian and International Pilots Association of getting its facts wrong and threatening legal action if it continues to disparage the carrier's staff.

But the union accused Mr Joyce of employing a divide and conquer strategy to erect a wall between Qantas mainline and Jetstar pilots.

In a strongly worded memo to staff, Mr Joyce branded as frivolous Australian Federal Court action by the union, which is claiming Jetstar's current operation breaches the Qantas Sale Act. He said the airline would vigorously defend its brand.

"We believe this Statement of Claim by AIPA has no merit, is frivolous and if it continues, will waste both the dollars of the union and its members and generate unnecessary costs against our company," he said.

But he said it was the rise in disparaging remarks against management, the airline's capabilities and personnel that was particularly galling.

"I can assure you that the company will do what it can to support any Jetstar employee who feels that their professional and personal integrity is being publicly challenged by AIPA and its spokespeople," he said.

"This includes potential legal action against the association where deemed appropriate. As CEO of the airline I will not stand for AIPA publicly making false statements against individual employees."

As an example of allegedly false statements, Mr Joyce cited the claim that Jetstar's general manager, flying operations, was a seconded Qantas second officer when, in fact, he was an experienced captain. He said this was one of five incorrect claims made by the union in recent weeks, including statements in a Senate committee about pilot licence renewal and the amount of time taken to complete command training.

"Ongoing comments by AIPA over the 'polluted culture' of the airline are simply ridiculous and show the depths the association is prepared to go to discredit our airline and our people," he said.

"The accusations by AIPA conveniently disguise an industrial relations campaign that, as you can see, continues to raise false and unsubstantiated claims against Jetstar."

AIPA has about 30 members in Jetstar, but does not have formal coverage within the airline and is not a party to the existing collective enterprise agreement.

Agreements are negotiated with the Jetstar Pilot Council, although the Australian Federation of Air Pilots represents 120 pilots and is a party to the airline's agreement.

The AFAP is also at loggerheads with the AIPA over its attempts to gain coverage of Jetstar pilots and has accused it of being hypocritical by attacking Jetstar members and at the same time seeking to represent them.

"We have the view that the Jetstar pilots have sought employment and have been given employment in a format they wish to undertake and we support them," AFAP industrial officer Lawrie Cox said.

But AIPA general manager Peter Somerville said the interests of Qantas mainline and Jetstar pilots were far more closely aligned.

He said Jetstar management was "obviously worried" and that AIPA wanted good careers for all Qantas Group pilots.

"We want to give Jetstar pilots access to Qantas mainline flying and promotional opportunities in circumstances where Joyce and (Qantas chief executive Geoff) Dixon won't let them," he said.