About 40 jobs will go from the former Farmlands head office in Hastings as it locks in savings from its merger last year.
Members of the South Island's CRT and the North Island's Farmlands voted to merge in February last year after being told there would be $38 million of net benefits over three years, with 42 per cent coming from the elimination of duplicated systems and resources.
It was described as the perfect marriage, because they were similar organisations but operating in different parts of New Zealand.
Staff were warned last month that the farm-supply company was consolidating functions and many jobs could go.
In a statement, the company said after considering staff feedback on the job losses "the rationale from the proposal around the location of support functions is largely unaffected".
"The Executive Leadership Team has decided to proceed with the proposal to centralise processing functions into the existing Dunedin Business Centre and the administrative support into the Christchurch Business Centre.
"The existing Hastings site will become the Hawke's Bay East Coast Regional Centre for customer facing functions.
"The Executive Leadership Team are now entering Stage 2 of the consultation process with individual staff which they hope to complete by the end of May 2014."
Many staff had seen the writing on the wall and had already left the Hastings office - there had been 120 working there before the merger, an employee told Hawke's Bay Today.
Many were offered jobs in other parts of the country. Farmlands is centralising processing functions into its Dunedin business centre and administrative support in Christchurch.
It released its first post-merger annual report in November, recording turnover of $2.17 billion for the year to June.