JLP head of press and PR Helen Dickinson said The SPA Way did not take part in the review process, but that its corporate work for the firm is unaffected.
Mantra joint MD Debbie Wosskow confirmed two staff had been made redundant, in what she described as a 'small decision' as the agency - which now operates with a staff of 23 - looked to focus on existing tech clients.
'In the current climate we have to work out the type of business we focus on,' she added.
Wosskow will head the Mantra account team, reporting to Dickinson and John Lewis Direct managing director Murray Hennessey.
Mantra has handled corporate work for the site since aiding John Lewis's acquisition of agency client Buy.com, the retail site that folded into the John Lewis Direct brand last year.
A pitch process last month took place with the aim of consolidating the client's PR work into one agency for corporate and consumer PR.
The combined corporate and consumer brief is understood to be worth a six-figure sum.
John Lewis retains Stephanie Churchill PR for its in-store soft furnishings PR and Citigate Smarts to promote its outlets in Scotland.