Prof Barker had initially been appointed for an 18-month term after Prof Keith Hunter retired in 2016.
Vice-chancellor Prof Harlene Hayne said Prof Barker had done ''an outstanding job'' over the past 18 months, providing ''excellent leadership'' for the division.
Prof Barker said he was eager to continue strengthening Otago's ''world-class sciences division''.
A project had recently begun to develop a strategic investment plan for the division ''that will take us through the next decade and beyond''.
Otago was the country's ''most science-intensive university with fantastic natural assets and people'' and it was a ''great privilege'' to lead the division, he said.
His research interests include statistical theory, methods and analysis for applications in areas such as fisheries and wildlife ecology, sport science and exercise physiology and climate change.
Prof Barker is a director of Dinsdale Ltd, a Manawatu agribusiness, and a director of Oritain Ltd, a Dunedin company that specialises in food tracing using trace-element and stable-isotope technologies.
