At least a dozen players will be kept out of Tuesday's match at Selhurst Park with the illness.
"The virus is spreading, we're disinfecting areas of the club," said manager Dougie Freedman. "Everyone has been on antibiotics.
"I think we are going to have to get the different units together separately – defenders, midfield and forwards – and coach them that way."
Palace famously beat Manchester United 2-1 at Old Trafford in the last round to set up a tie with their Championship rivals.