The club captain has not featured for the Premier League's bottom side since August 17 because of a knee problem and is not likely to return until after next month's international break.
"I love Deeney, you all know that, and we know how he can help the team, but right now he is not the solution," he told a press conference.
"He has a lot of character and represents well the values of the club: be organised, be brave, be compact and solid. This is the character we want."
Sanchez Flores has received some good news with Isaac Success returning to fitness after a groin problem, while midfielder Etienne Capoue (back) is not 100 per cent but is in contention to face Chelsea at the weekend, as he looks to rectify a run of just one goal in five matches in all competitions.
"We need to talk about the solutions as these players are not ready right now," said Sanchez Flores.
Sanchez Flores will also get a lift from the arrival of Joao Pedro after the Brazilian received a work permit to join in January.
"I saw him play and he is strong, really quick and he scores goals," said the Spaniard, whose only victory in eight matches since taking over came in the Carabao Cup against Championship side Swansea.
"January is so far away right now – the focus is on what happens in the next two days. We love the player but he is not the solution right now."