The Argentine was withdrawn just before the half-hour mark during Saturday's clash with Almeria but the club is yet to determine the extent of the problem
The Argentine star had opened up the scoring for Tata Martino's side in the 21st minute, but was withdrawn shortly afterwards with a knock.
And it has now been confirmed that he has a thigh problem, but the club is yet to determine how long it will be missing the 26-year-old.
"Messi picked up an injury during the match against Almeria this afternoon," a statement on the club's official website reads.
"The Barcelona forward sustained an injury to the biceps femoris in his right thigh and he will undergo additional tests on Sunday to determine the severity of his injury."
Messi has suffered numerous injury problems of late, most notably when a hamstring problem kept him out of several matches at the end of last season.
His most recent knock renders him a serious doubt for Tuesday's Champions League trip to Celtic.