Messi, 33, has scored just once -- a penalty against Villarreal -- in four games this season after agreeing to stay at Barca until at least the end of his current contract, which expires in June 2021.
"Maybe, at the moment, Messi's performances could be better," the Dutchman said ahead of Barca's return to European action against the Hungarian champions at Camp Nou on Tuesday.
"But he is happy, he is working hard and he wants to be the captain. I don't have a single complaint. He has also had some bad luck. He hit the post [in Saturday's 1-0 loss to Getafe] and on another day that goes in.
"I don't have any doubts about his performances and we're going to see him [at his best] in the upcoming games, I'm sure."
Despite that, exits at the hands of Roma, Liverpool and Bayern in the last three years still haunt the club. Koeman said Barcelona can no longer be considered the outright favourites to win the competition because of that.
"I can't explain what happened in recent seasons because I wasn't here -- there were different players and coaches -- but if we fail this season, I will be able to tell you why," Koeman said when pushed on Barca's Champions League struggles since last lifting the trophy in 2015.
"But seeing what's happened in recent seasons, I can [say] we are not the favourites. We are one of the teams that can go far in the competition, but not the favourites."
Barca are then back in league action on Saturday when they host Real Madrid at Camp Nou in the Clasico. Both teams go into the fixture on the back of defeats at the weekend.