The University of Western Australia's vice-chancellor is stepping down from the role, saying he has chosen to decline a new contract offer from the institution.

Paul Johnson said he declined a new five-year contract from the university, after what he described as "a great deal of reflection".

Professor Johnson, who has served in academia for decades, has been UWA's vice-chancellor since 2012.

He came into the role following a four-year stint in the same role at Victoria's La Trobe University.

Professor Johnson said family reasons were a factor in his decision, saying he would remain in academia and keep living in Perth.

"UWA is at a key point of renewal, with the four new faculties and a new professional services structure commencing in January 2017," he said in a statement.

"I think this is an opportune moment to hand over the leadership to someone who can further build on the many achievements of recent years, and carry renewal forward to create new opportunities for this great university."

Professor Johnson attracted some controversy during his tenure, particularly relating to his support of a partnership at the university with Danish researcher Bjorn Lomborg.

That deal caused a backlash within the UWA staff and student body due to Dr Lomborg's stance on climate change. Professor Johnson eventually backed down.

He was also at the helm of the university when it announced in late 2015 300 staff would be laid off as part of sweeping cuts aimed at reducing costs.

Professor Johnson said the university would commence a "global search" for his successor in the near future.