The Argentine World Player of the Year, joint top scorer in this season's competition with eight goals, had an injury scare on international duty and was only used as a substitute in the 1-0 La Liga win at Villarreal on Saturday.
"In Villarreal I did not feel good," Messi told a news conference on Tuesday at Barca's Nou Camp stadium.
"I'll work as hard as possible so that the discomfort disappears and little by little I feel better."
Messi warned against underestimating Ukraine's Shakhtar, who shocked Barca 3-2 at the Nou Camp in the group stage in December 2008.
They also pushed the Catalan club all the way in the European Super Cup in 2009, eventually losing 1-0 to a Pedro strike in extra-time.
"We know it will be a very tough game as we are facing a team that has some great players and that knows how to play very good football," Messi said.
"Matches against Shakhtar are always very close," he added. "You just have to look at the result in the European Super Cup and the last few games we have played them.
"We'll have to go out there very focused as otherwise they could surprise us."
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