Staff members were asked to vote on whether they supported a deferral of a 2 per cent wage increase for two consecutive years after the university reported a $225 million funding shortfall due to the coronavirus crisis.

ANU vice-chancellor Professor Brian Schmidt said if the Fair Work Commission endorsed the deferral, it would save $6.75 million this year and $13.5 million over 12 months but more budget cuts would be necessary.

"This saving directly translates into being able to keep more jobs, and we will transparently demonstrate how every dollar will be used to protect jobs," Professor Schmidt told staff in an email.

"I acknowledge the selflessness and community spirit that led so many staff to support the deferral.

"While today's decision will help us retain more jobs into the future, it does not resolve all the issues we face. We still need to reduce our costs further. We are going to do as much as possible through voluntary separations, and we will reduce or defer spending wherever we can.

"I commit to work with union representatives and leaders, as I know they share my goal of achieving that objective with the minimum hardship on our staff."

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He said the deferred pay increase would be paid next year and staff who were eligible for a salary increment this year would receive it.

The decision will delay the 2 per cent pay increase scheduled in July 2020 to July 2021, and delay the 2 per cent pay increase scheduled on July 2021 to July 2022.

A total of 4217 staff voted in the ballot, representing 60 per cent of the total staff population.

The university will put the variation to the Fair Work Commission to have the variation to the enterprise agreement formally approved.

National Tertiary Education Union ANU branch president Matthew King said the result showed staff were divided on the issue.

"This is a very narrow defeat, but it is also far from a decisive mandate for proceeding with this proposal. The next steps are not automatic. ANU will now have to make a conscious decision, after reflecting on the narrow margin of the vote, to proceed to the Fair Work Commission to implement these changes.

"It is clear ANU staff are divided on whether it would be best to do so."

NTEU ACT division secretary Dr Cathy Day said the 'no' campaign the union ran leading up to the vote raised important concerns in relation to equity, protecting jobs and financial transparency.

"While we're disappointed with the result, this campaign has managed to win some commitments from ANU and we'll turn our attention to holding management accountable for saving jobs.

"We'll also be preparing to ensure that the generosity of ANU staff during this crisis is reciprocated during Enterprise Bargaining."