Former WA Scientist of the Year Jorg Imberger has been suspended from his post at the University of Western Australia amid an investigation into serious misconduct allegations.

Professor Imberger, who has worked at UWA for 50 years, launched Federal Court proceedings under fair work laws on Friday after receiving a letter on November 17 informing him of his suspension on full pay.

Court documents reveal the letter from UWA senior deputy vice-chancellor Professor Dawn Freshwater said former students of the Centre for Water Research, which Professor Imberger directs, had made allegations relating to claimed breaches of the university's code of conduct.

The letter did not outline any details of the allegations but said they would constitute serious misconduct if substantiated.

Professor Imberger was given five days to respond.

He was later told an investigation had been commissioned into the allegations.

In the Federal Court yesterday, Professor Imberger lost a bid for an injunction allowing him to return to full duties pending the outcome of his action under fair work laws. His action alleges the university has denied him procedural fairness and contravened the Fair Work Act.

Yesterday, lawyer Greg McIntyre argued the university had failed to follow proper procedure in the suspension and his client should be granted an injunction.

Federal Court Justice John Gilmour said he was surprised somebody of Professor Imberger's standing in the academic community could be suspended by a letter that gave absolutely no indication of the nature of the allegations against him.

Justice Gilmour described Professor Imberger's work in the field of water research as impressive and noted that the long-serving academic had been deeply distressed by the situation.

He said Professor Imberger denied the allegations and his suspension did not mean there was "any substance whatsoever" in the claims.

Justice Gilmour accepted there was a serious issue to be tried in Professor Imberger's substantive case, but rejected his application for an injunction.

UWA lawyer Ian Neil said the university would formalise its position on the allegations and put them to Professor Imberger by the end of this week.

He said the university was prepared to relax the suspension to allow Professor Imberger to continue research work, but did not want him representing UWA and having contact with students while the investigation was conducted.