Writing in the university magazine, Sir Alan Langlands, the principal and vice-chancellor, said the institution needed to identify savings of just over £3 million.
Already, about 100 staff have taken voluntary redundancy or had their hours cut as part of the university's sustainability review, which began before last year's budget. The budget gave Scottish universities a £30 million increase in funds - £138 million less than requested.
Mike Pittilo, principal and vice-chancellor of The Robert Gordon University, warned of job losses after the budget, but Sir Alan is the first head to say staff must go.
"Given the disappointing outcome from the Government's Comprehensive Spending Review and the pressures on pay, pensions and utility budgets, the action taken following the university's own sustainability review and delivery of the targets set in our strategic framework will move us towards a break-even position," Sir Alan said.
"This puts a premium on achieving savings through voluntary severance and generating additional income through improved research overhead recovery and expansion of taught postgraduate provision.
"Action in these three areas is already resulting in significant improvements to the university's financial position, and this will have to continue," Sir Alan said.
A spokesman said the university anticipated that staff levels would return to current levels by 2010-11 as funding was found elsewhere.
Tony Axon, spokesman for the University and College Union, said: "They (universities) shouldn't be so quick to react to this budget, particularly in the first and second year of this funding, because there is an opportunity to get better funding in the future and ride the storm."