The group, which is hosting a strategy day, said that it does not expect to make a half year profit, while profits for the full year will come in “substantially” lower than last year.
Waitrose will exit four convenience shops and one small supermarket.
Sir Charlie Mayfield, chairman of the John Lewis Partnership, said: “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 company pointed to “market uncertainty” and cited significant extra costs at the partnership as a result of “greater IT investment”, which it said will be a big driver behind the profit change.
Waitrose is expected to see profit growth and John Lewis a decline.