The Warehouse Group has "realigned" its online shopping division and 40 staffers will be affected by the change.
The retailer hopes that most of the employees will be re-deployed into other roles.
Warehouse chief executive Pejman Okhovat told the Otago Daily Times that the retailer was making changes to its business to"remain relevant to our customers as their shopping behaviours change".
Okhovat did not answer when asked if the online centralisation of jobs, understood to be to Christchurch and Auckland, was connected to Amazon's proposed entry to New Zealand and Australia.
The US online shopping giant's pending incursion into Australia and New Zealand already has retailers concerned about loss of market share.