An F-35 fighter jet.

Cuts to the Defence Science and Technology Organisation: An F-35 fighter jet.

Nearly 40 of Australia's top military scientists and engineers are to be thrown on the scrapheap as the Defence Science and Technology Organisation cuts costs.

The jobs cull is expected to  cut from six scientists to just two the DSTO's technical team for the $24 billion Joint Strike Fighter, the nation's largest ever defence purchase.

<i> Illustration:Cathy Wilcox.</i>

Illustration:Cathy Wilcox.

The Australian Maritime Warfare Centre, based at Sydney's Garden Island, is slashing a third of its staff of civilian engineers and technicians, from 48 public servants to 31.

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DSTO is "spilling" 199 position among its senior research leaders with 38 of them expected to be cut loose.

The 38 technical specialists based in Canberra, Melbourne and Adelaide have been told their status is “unassigned”, a step on the way to being declared “excess” and many of them have already been asked to apply for voluntary redundancies.

The engineers' and technicians union Professionals Australia is warning that hundreds of years of experience in defence science will be lost as a result of the cuts and called on DSTO bosses to reconsider. 

"Many of these guys have been blindsided as they have been strong performers and are involved in relevant, ongoing research and capability support,'' spokesman David Smith said.

"They are senior research leaders with hundreds of years of science expertise and international reputations.

"In most cases, there would be a handful of scientists across the country that would have the appropriate skills to do their work at a high level so the cost of contracting in additional skills at some stage will be very high.''

The cuts are part of a wave of redundancies set to hit the Defence establishment in Tuesday's budget.  The department's procurement arm, Defence Materiel Australia, is set to be slashed and then merged into the broader department.

The Defence headquarters at Canberra's Russell offices was buzzing with talk on Monday that up to 5000 civilian jobs would be lost.

The Joint Strike Fighter, or Lockheed Martin F-35 Lightning II, is a ''fifth generation'' stealth warplane being developed for the US and nine allied countries including Australia.

The Abbott government committed in April to buying 58 of the aircraft with a price tag of $24 billion over the operational life of the fighters, despite persistent technical flaws on the project.

While nearly all of the technical work on the fighter jet project is being done by its manufacturer Lockheed Martin, Mr Smith argued that it was vital that the Australian Defence establishment maintain its expertise on the project.

“Cutting from six to two (technicians) just leaves DSTO so exposed,” Mr Smith said.

“If this goes ahead then the only people who’ll be the experts on the plane will be ones they’d have to contract in.”

Mr Smith was also scathing of the sackings of the Maritime Warfare Centre at Garden Island, saying the move  goes against advice the government had received.

"All defence reviews have recommended they need more public service Navy engineers, not less," he said.