"Messi will definitely miss the game against Villarreal after doctors confirmed on Tuesday that the player is still feeling some discomfort from his muscle injury," the club said on their website.
The 18-year-old Argentinean has been out since the second leg of the Barca-Chelsea tie in the first knockout stage of the Champions League.
He was expected to make a comeback against Villarreal, who play the other semi-finals tie against Arsenal, but this setback may mean that he won’t be ready for the San Siro game.
"Messi, who was absent from training on Tuesday afternoon, will continued with treatment to recondition the affected muscle until he is able to return to normal training," the club said.
Swedish international striker Henrik Larsson has replaced Messi in the starting line-up since the later was sidelined in March and he is most likely to start alongside Samuel Eto’o and Ronaldinho against Milan.