Otago's percentage of female professors and associate professors had increased from 15.6% in 2007, but only Lincoln University had a worse current ratio of 17.1%.
Otago had the lowest percentage of female professors this year (13.3%), according to data published in the latest New Zealand Census of Women's Participation.
The university had 32 female professors and 68 female associate professors.
Waikato University had the highest percentage (29.59%) of female senior academic staff and the highest number of female professors (23.8%).
Equality for women in pay and job opportunities was a topic of discussion in Dunedin last week, when lawyer and former Massey University professor Dr Judy McGregor visited the city. She said New Zealand women still had a long way to go to gain full equality.
Dr McGregor, the Equal Employment Rights Commissioner, participated in a two-day national symposium for aspiring female leaders in tertiary education at the University of Otago.
She felt "frustrated" and somewhat "grumpy" that many women were still not being paid equally for their contribution to the national workforce, including in the public sector.
Dr McGregor had been the Equal Employment Opportunities Commissioner at the Human Rights Commission for a decade and prepared the recently-published women's participation census, having also initiated the series.
She told those at the New Zealand Women in Leadership symposium about her "worry" that New Zealand women were still not achieving full equality, despite the many women graduating. Women comprised less than 25% of the country's senior tertiary academic staff.
Dr McGregor acknowledged several positive aspects of Otago University academic life, including transparency over professorial pay rates.
Some overall progress was being made, but New Zealand women were still lagging too far behind, including in company boardroom representation, she said.
Women should not have to wait further decades to achieve full job and pay equality, she said.
Otago University vice-chancellor Prof Harlene Hayne also spoke at the symposium, about continuing efforts to support staff families, including through improved child care facilities. She said more than half of Otago students were women.