University of Adelaide vice-chancellor Peter Rathjen has taken an indefinite leave of absence less than 24 hours after chancellor Kevin Scarce resigned without public explanation yesterday.

In an email to professors this morning, the university's provost, Professor Mike Brooks, said the University Council had endorsed Professor Rathjen to take "special leave for an indefinite period".

Professor Brooks will be acting as vice-chancellor in his absence.

Yesterday, chancellor and former SA governor Kevin Scarce told the university’s board he was resigning with immediate effect, cutting his term six months short.

The university has refused to comment on why either man stepped away from his position.

"In his absence, the university has appointed Professor Mike Brooks as acting vice-chancellor. Professor Brooks has previously served as both acting and interim vice-chancellor.

"The university's world-class education and research is continuing."

Asked why Rear Admiral Scarce cut his term short yesterday, the spokesman said he had "made his own decision to shorten his final term as chancellor".

"The university's deputy chancellor has issued a statement about the chancellor's contribution to the university and has no further comment to make on his decision."

The ABC has contacted Rear Admiral Scarce and Professor Rathjen for comment.

The National Tertiary Education Union said the resignation of the chancellor and the vice-chancellor's leave of absence came as a shock to staff.

"University of Adelaide staff desperately need clarity from the University Council and the remaining senior management on why the chancellor has resigned and why the vice-chancellor is taking indefinite leave," the union's Adelaide branch president, Nick Warner, said.

Deputy chancellor acknowledges 'significant contribution'

In her statement, deputy chancellor Catherine Branson thanked Rear Admiral Scarce for his "significant contribution" to the university since 2014, describing him as a "strong presence and advocate for the university".

"On behalf of the [university] council, I thank Rear Admiral Scarce for his significant contribution to the university over almost six years," the statement read.

"As chancellor, he has led council during an important time of transition, when the university's world rankings and its role in the South Australian community have continued to rise.

"His term as chancellor has encompassed the opening of the state-of-the-art Adelaide Health and Medical Sciences building, which is a critical part of the Biomed City Precinct, the adoption of a new strategic plan and a stronger focus on outcomes for South Australia's industry and community."

Rear Admiral Scarce preceded current Governor of South Australia Hieu Van Le and led the Weatherill government's nuclear fuel cycle royal commission.