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However, the university has categorically denied the suggestions, saying they are "definitely not true" and cuts to the department are not planned, either now or in the New Year.
Separate sources spoke to the Otago Daily Times saying morale was variously at "rock bottom" in the department and the rumours that jobs were going were "very unsettling" for the "good, young" team of academics working there.
The allegations come after a recent proposal to make cuts to the department of marine sciences, which would review eight academic positions reviewed and remove three full-time academic positions if it went ahead. Division of Sciences head Prof Richard Barker firmly denied the suggestion, saying a proposal to cut jobs was "definitely not true nor is it planned".
Submissions on the proposal closed last week.
Environmental groups, other marine science academics from New Zealand and overseas, and international collaborators and students have made submissions protesting the loss of three academic jobs.
A decision is expected on the proposal by the end of November.
Department staff have set out their own proposal to reduce the department's deficit, in which head of department Prof Steve Dawson has opted to take early retirement.
Their proposal set out alternative suggestions to reduce the marine sciences deficit, which is due to reach $4.2million by the end of the year.
The Tertiary Education Union declined to comment on the rumoured cuts.