The Lowitja Institute announced the appointment of Paul Stewart as its new chief executive on Tuesday, taking over from Janine Mohamed, who stood down from her role in March.

Mr Stewart, a Taungurung man with connections to Central Victoria, will lead the country's only national Aboriginal and Torres Strait Islander community-controlled health research institute.

His career has spanned over 20 years across a range of sectors - including First Nations health - and he has longstanding ties to the institute, both in his early career in Indigenous health research, and more recently as deputy and interim chief executive.

Mr Stewart said he would endeavour to continue on the legacy of the organisation's "remarkable leader" and namesake, Dr Lowitja O'Donoghue, who passed earlier this year.

"I am committed to honouring her legacy to support health research that is led by our people, for our people," he said.

"I also want to thank Adjunct Professor Janine Mohamed for her leadership and mentorship over the years – and I look forward to continuing our work to drive positive change to improve outcomes in Aboriginal and Torres Strait Islander health."

Chair Selwyn Button said the Board was proud to appoint Mr Stewart, who has played a "key role in championing Aboriginal-led research for our peoples."

"He brings a wealth of experience in strategic leadership," Mr Button said, "as well as an understanding and commitment to supporting our community-controlled organisations across the country."

"We look forward to working with him to further strengthen the Institute's role to support community-led research, and influence health research policy reform for our mobs."

Co-patron of Lowitja Institute, alongside Dr Lowitja O'Donoghue, Pat Anderson also expressed her support for Mr Stewart in his new role.

"I am very happy about this appointment," Ms Anderson said.

"Paul has been with Lowitja Institute for a number of years as deputy chief executive and has shown dedication and commitment to social justice in health."

She said she first met Mr Stewart when he was working for ONEMDA, the Aboriginal and Torres Strait Islander Health and Wellbeing, under Professor Ian Anderson at the University of Melbourne.

"I look forward to continuing the important work of the Institute with Paul in his new role as chief executive officer," Ms Anderson said.

Mr Stewart begins his role with immediate effect.