The company said it does not expect all of its 42 shops to reopen at the end of lockdown and will make a decision at the end of March.
Recent reports suggested eight stores were earmarked for closure, on top of eight announced in July.
The group also scrapped its staff bonus for the first time since 1953, as previously reported, after the coronavirus crisis sent it plunging to a loss for the year to January 30.
A JL spokeswoman did not rule out Sheffield from among the proposed closures.
The uncertainty will be a blow to staff, the city centre’s retail offer and the city council - which has paid £3.4m to buy the lease on the firm's Barker’s Pool premises and agreed to pay for a ‘comprehensive refurbishment’.
The authority is keen to retain the department store as part of its £480m Heart of the City redevelopment scheme.
It comes after the pandemic led to the permanent closure of a string of shops in Sheffield including the Debenhams department store on The Moor. It will reopen after lockdown to sell stock before closing permanently.
John Lewis chairman Sharon White said there was no getting away from the fact that some areas could not ‘profitably sustain’ a John Lewis store.
She added: “Regrettably, we do not expect to reopen all our John Lewis shops at the end of lockdown, which will also have implications for our supply chain.
“We are currently in discussions with landlords and final decisions are expected by the end of March.
“We will do everything we can to lessen the impact and will continue to provide community funds to support local areas.”
She added: ”All our John Lewis stores need to be exciting places to shop, more reflective of the tastes and interests of local customers. This will require investment and we are working closely with landlords and local authorities. We are keen to play our part in the revitalisation of the high street.