Paris Saint-Germain supporters jeered Messi and Neymar during a Ligue 1 match against Bordeaux that followed their Champions League elimination at the hands of Real Madrid.
The Argentina superstar has scored nine goals and supplied 13 assists in 32 appearances in all competitions for PSG – an underwhelming return in the wake of his blockbuster arrival from Barcelona.
A total of 22 goal involvements is his worst output since the 2006-2007 season, which was just his second full campaign at the highest level.
Messi's numbers could have been higher, with the 34 year-old having been denied by the woodwork a record 10 times in Ligue 1 alone.
Karembeu, a World Cup and European Championship winner with France during his playing days, thinks Messi should be given an undisputed leadership role at PSG to help him flourish.
"When Messi plays and wherever he goes, everything is always full on. It's like this in France," he said. "He is a sensational player, but he is also an attraction for the French league. Messi is more than a player. We have to respect this guy more in France, because he attracts people. It's very important.
"You can't whistle Messi because he's a star. It is a mistake by the fans, because if the crowd offers him affection he will end up standing out.
"It wasn't easy for him to leave Barcelona. What I'm going to say depends on the coach, but for me Messi has to be appointed the leader of the group at PSG.
"If PSG let him lead, guide and take care of the group, they will always win. But they have to let him be the leader.
"Messi has to be the leader to show his football. We saw it for 20 years at Barcelona, so it won't change. He has to go down that path, where he is the technical and group leader.
"He has to be the captain because he knows his role perfectly. Messi is a magician and we have to stop judging him because we know that when he touches the ball, something will always happen."