Prop Mullan suffered an elbow injury in his side's 38-22 win over Northampton Saints in the Aviva Premiership, while centre Daly went off with a knee problem in the same game.
The duo will not travel to the camp in Portugal with England and instead will remain with their club to get furthers scan and treatment on the injuries.
England head coach Eddie Jones has decided not to call up any replacements for the duo who may still make it in time to play in the autumn internationals.
The Red Rose first play Argentina at Twickenham on November 11 before a clash with Australia on the 18th and then rounding out the autumn schedule with a game against Samoa on the 25th.
Jones' squad has already seen a few surprise decisions with experienced flanker James Haskell left out completely from the 34-man group.