Messi was flattened after receiving a blow on his left leg in the 3-1 win over Napoli in the reverse fixture of their Champions League clash on Saturday.
Khalidou Koulibaly aimed to clear a ball from his box before Messi sneaked in his front to touch the ball from behind and the Napoli defender hit Messi on his calf.
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Barcelona was awarded a penalty and Luis Suarez converted the spot-kick with Messi still to gain his balance.
Setien has confirmed there won’t be a problem with regards to Messi’s participation against Bayern Munich in the quarter-final of the Champions League on Friday.
”Messi? He had some pain, but there shouldn’t be a problem,” the Barcelona head coach said when asked if Messi had recovered.
“He was fine. We will analyse it, but there won’t be a problem.”
Looking ahead to the game against Bayern Munich, Setien admitted it will be a “complicated” tie, but praised his side for their performance against Napoli.
“The game against Bayern Munich will be complicated, but we are also a great team,” he added.
“The team has been good and we deserved the victory. We have overcome the opening minutes and in the second half, Napoli didn’t create much danger.
“The truth is that Napoli is one of the best Italian teams. We knew how to react to their start and then we had a good first half.
“They have had more prominence during the second half.”