The staff will be made redundant from its East Malling and Wye sites, following similar moves at sites in Wellesbourne, Kirton and Efford.
The reduction in staffing levels is described as necessary to ensure HRI can remain stable and financially viable.
The move follows a recommendation made by the five-yearly review of HRI which said an independent research operation should be set up to preserve work of HRI East Malling and Wye.
A five-year business plan by the East Malling Trust for Horticultural Research has now received a positive response from DEFRA minister Lord Whitty. The new organisation will be known as East Malling Research.