The brains behind inventions like newborn hearing tests and Boeing's new Dreamliner plane fear similar innovations in the future could be lost.

The Federal Government's Commission of Audit has proposed merging Cooperative Research Centres (CRCs) with the Australian Research Council (ARC).

The centres are industry-based bodies that develop solutions for business, and advocates fear the proposal would push them into academia.

CRCs link bright ideas with industry, with the goal of turning innovations into practical solutions.

Hearing CRC CEO Associate Professor Bob Cowan said the CRC program was fundamentally different to any other research program that existed in Australia.

"All of our projects have identified end users who are involved in framing the project, who are involved in carrying out the project, who are involved in applying that technology and the outcomes of that project directly into clinical practice," Professor Cowan said.

CRCs have helped design wing parts for Boeing's flagship 787 Dreamliner and a technique to improve mining productivity, saving millions of dollars.

CRC Association chief executive Dr Tony Peacock said the shift to the ARC would remove industry input from the process.

"[Australians] are great at ideas but we're not great at the execution of those ideas," he said.

"You don't want to be always about discovery and always new things. You've got to bed down some of the things you've already discovered."

ARC head Professor Aidan Byrne says his organisation does have the capacity to run the centres, should the Government accept the Commission of Audit's recommendation.

"The CRC program is actually a very good program for the country," he said.

"[But] it's coming back to, I think, what the Commission of Audit is all about, trying to identify duplication of functions across government.

The Industry Minister declined to respond prior to next week's budget.

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