The group, which is hosting a strategy day, said it does not expect to make a half-year profit, while profits for the full year will come in "substantially" lower than last year.
It bemoaned "market uncertainty" and cited significant extra costs at the partnership as a result of "greater IT investment", which will be a driver of the profit decline.
John Lewis cuts staff bonus as profits plungeWaitrose will shut four convenience shops and one small supermarket, affecting around 200 staff.
The Waitrose stores that are closing are:
Colemore Row, Birmingham
Portman Square, London
Sir Charlie Mayfield, chairman of the John Lewis Partnership, warned that the malaise "isn't a blip".
He added: "It is very important that we feel the jeopardy of what is happening right now.
"This isn't a blip, it is a major shift and it has a while to run."
The photos which show the devastation caused by the Saddleworth Moor fireWaitrose is expected to see profit growth and John Lewis a decline.
The firm added: "It is widely acknowledged that the retail sector is going through a period of generational change and every retailer's response will be different. For the Partnership, the focus is on greater differentiation - not scale.
"We have clear plans to build on our strengths and to sharpen our points of difference in both Waitrose and John Lewis."
Retailers have been hammered by rising costs and falling consumer confidence, with several high-profile casualties this year resulting in hundreds of store closures.