PSA national secretary Richard Wagstaff said the scale of the proposal, which would reduce staff numbers by about 15 per cent, had taken staff by surprise.
"In an organisation of its size with only about 72 full-time staff, that's a pretty big hit and will have significant flow-on effects in terms of workload and efficiency."
Mr Wagstaff said staff were also unsettled by the suggestion the commission's head office could be moved from Auckland to Wellington.
He said the "lop-sided" approach of the review would increase the number of management positions.
"The commission has always had plenty of well-paid managers and this appears to be a classic case of building up managers and cutting workers.
"There are also concerns that the strategic direction outlined in the review will impact on the commission's ability to proactively work with the community in ensuring everyone's human rights are protected and upheld."
Mr Rutherford said the review would result in an effective and financially sustainable organisation which was well positioned for the future.
"This proposal is about making strategic decisions about where we can make the biggest difference for human rights in New Zealand Aotearoa and this is where we will focus our people and our efforts. It is not about reducing our services."
Staff would be consulted before a final decision was made by the end of May.