Serco is seeking to shed 36 posts on its routes from Aberdeen and Scrabster in Caithness to Stromness and Kirkwall in Orkney, and Lerwick on Shetland.
A ballot for industrial action over working terms and conditions was cancelled in the summer.
The National Union of Rail, Maritime and Transport Workers (RMT) said it would not accept any compulsory redundancies among the 350 workers affected by the move, with negotiations due to start next week between the union and the company.
Stuart Garrett, managing director of Serco NorthLink Ferries, the new title of the operators, said the company had begun its formal consultation with seafaring staff and unions on its ferries with a view to reducing staffing levels by up to 36 jobs.
He said: "We plan to adopt flexible crewing levels, allowing us to tailor staffing levels to passenger numbers. This is a common procedure with nearly every other commercial ferry operator in the UK. Safety will not be compromised; the staffing arrangements we propose continue to exceed the crew-to-passenger ratio required for our vessels by the Maritime and Coastguard Agency. The consultation with staff will look at all available options. We are hoping to achieve these changes without the need for compulsory redundancies."
Mike Hogg, the RMT's regional shipping organiser, said any move to compulsory redundancies would be resisted, with a ballot for industrial action if necessary. The union represents the majority of the staff, apart from the ships' officers.
Mr Hogg said: "We have just been advised of the potential reduction in manpower. This obviously concerns us greatly because it was only in the summer we cancelled the ballot for industrial action we had called to protect jobs, conditions and pensions. But we got guarantees from Serco which satisfied us.
"We are happy to enter meaningful discussions with the company in order to find the best solution for RMT members. But one thing the RMT is absolutely clear about is that we will not accept or tolerate any enforced redundancies.
"We have a meeting scheduled with the company for them to explain the rationale behind the proposed reductions, as we are keen to maintain a working relationship with Serco. But not at any price."
Meanwhile, Serco announced this week that freight and passenger fares would increase by 2.8% next year, as agreed with the Scottish Government
It will also reduce off-peak sailings from Scrabster to Stromness from three sailings each day to two.
The controversial multinational, which specialises in managing outsourced Government contracts, won the new £243 million six-year Northern Isles ferry contract in May. It took over from the publicly owned NorthLink Ferries, part of the David MacBrayne Group, although the vessels are owned by a subsidiary of the Royal Bank of Scotland.
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