Flood injured a hamstring in Tuesday's League Cup penalty shoot-out win over Alloa and a scan showed he had torn the muscle.
Flood will be joined on the sidelines for Saturday's Scottish Premiership clash with St Johnstone by forward Josh Magennis and winger Jonny Hayes, who spent the night in hospital after getting a head knock against the Wasps.
Manager Derek McInnes said: "Josh has got a shoulder problem. He landed on it in training on Monday and didn't think too much of it and reported on Tuesday morning with real acute pain. He can't have any contact so he is out as it stands.
"Jonny is okay but because there's been a concussion he won't be available for the weekend."
McInnes is looking for his team to turn their possession into goals as, following a 2-1 defeat by 10-man Hearts last weekend, they failed to score in 120 minutes against their Scottish Championship visitors.
He said: "We had plenty of chances at Hearts and we didn't make the most of them and certainly against Alloa we did not make the keeper work nearly enough.
"We have got to make sure we buy a ticket more, have more shots on goal, get in better areas to score goals and get more bodies into the box.
"We have got to be more forceful and force the issue and we are all responsible for that.
"We had umpteen corners on Tuesday and we need to make more of set-plays as well as general play."