The trio are Distinguished Prof Neil Gemmell, of anatomy, Prof Michelle Thompson-Fawcett, of geography, and Prof Poia Rewi, former dean of Te Tumu, the School of Maori, Pacific and Indigenous Studies.
The fellowship recognises distinction in research, scholarship or the advancement of knowledge at the highest international standards.
Prof Gemmell was "internationally renowned" for his contribution to genomics, evolutionary biology, conservation biology and reproductive biology, a society spokeswoman said.
Prof Gemmell, who was awarded the society’s Hutton Medal last year, was recognised as the leading molecular evolutionist in New Zealand, and a leading researcher internationally in ecological and evolutionary genetics.
Prof Thompson-Fawcett was a world-leading specialist in advancing contemporary matauranga Maori (Maori knowledge) and fostering "indigenous approaches to culturally sustainable environmental futures", the spokeswoman said.
Her work with indigenous communities had generated pathways for holistic, integrated, intergenerational indigenous approaches that recognised relationships, environmental interactions and Treaty obligations.
Prof Rewi joined the Otago staff in 2003, became dean in 2015 and left the university last year to become chief executive of Te Matawai, a government agency supporting Maori language revitalisation.
He had co-designed with Prof Rawinia Higgins a Maori language revitalisation model which had since been incorporated into policy, had informed new legislation — Te Ture mo Te Reo Maori (Maori Language Act 2016) — and had been implemented to accelerate the learning of te reo in schools.