Messi scored a penalty to help the Catalan giants to a 2-1 victory at Camp Nou on Wednesday, a result that left them three points clear at the top of Champions League Group G.
A clip of the Argentina star failing to press the Dynamo defenders in second-half injury time went viral after the match, though, as viewers called the forward's work rate into question.
Messi had more shots (six) and created more chances (four) than any other player in the match, but he also lost possession more frequently than anyone else (20 times) without once winning it back.
His form has been scrutinised ever since he failed to engineer a transfer away from Barca in August and September. Despite attempting more shots (28) than any other player in La Liga, he has yet to score from open play in the competition in 2020-21 or provide an assist in his six appearances.
Koeman, however, says out-of-context footage is no way to judge a player's effectiveness and insists Messi remains an essential player.
1 - Lionel Messi's goal was his first against Dynamo Kiev since December 2009, with this being his longest gap between goals against the same opponent in the Champions League (3983 days). Bide. pic.twitter.com/paEgHcXP9g— OptaJoe (@OptaJoe) November 4, 2020
"I didn't seem him [walking] and I'm not interested in this because I don't see him walking," the Barca head coach said on Friday. "If you want to start a controversy around this point, it's your problem.
"Messi is mentally good, enjoying this sport. He's a winner and sometimes you go through moments when the ball doesn't go in, but he looks really focused on that subject.
"I think Messi still has so many qualities. He's very important in our game. He scored the penalty and we're used to him making the difference here, and he's still a very decisive player.
"You said [the footage was from] the 93rd minute - there are pictures of anyone, of me when I'm sitting down, or annoyed. It seems we should be more aware of our image than our work. I don't agree with that.
"I think these players, like those of my era, have the same effort as us. They work in training, they want to win and it annoys them when they don't win. If it were not like this, it'd be because my work isn't working."
Barcelona are 12th in La Liga having failed to win in their last four league games, but Koeman says people should stop obsessing about poor results so early in the season.
He said: "Teams like Barca have to be at the top, if you are not there there are criticisms, but we must not obsess over it. The season is very long and you have to work game by game. It is necessary to win, but it does not guarantee tranquility. In this club many things happen, we must be prepared for everything."
Barca face Real Betis at Camp Nou on Saturday, looking to record just their third league win of the season.
Veteran winger Joaquin caused a stir this week when he claimed he would not even hire Koeman "as kit man" after a difficult spell working under him at Valencia.
Asked about those comments, Koeman said: "I understand it's a really interesting topic for you. If he speaks, it's his problem. I'm focused on the game and not individual things that happened many years ago."