The company said the shake-up will take place as part of a simplification of store management.
It comes after a raft of recent job cuts, which included the closure of eight John Lewis stores earlier this year, in a bid to secure £300 million in savings by 2023.
The company currently operates 331 Waitrose stores and 34 John Lewis shops across the UK.
John Lewis Partnership said it will support employees who wish to stay in the business in finding new roles and will seek to minimise compulsory redundancies through voluntary redundancy and severance options.
A John Lewis Partnership spokesperson said: "We have announced to our partners our intention to simplify our management structures in Waitrose and John Lewis stores, which will allow us to reinvest in what matters most to our customers."