India drew the first Test which finished at the Gabba on Monday but Ganguly said he was concerned about Harbhajan's form.
Ganguly, named man of the match after his first innings 144, said the finger spinner was capable of playing better.
"I think he's a much better bowler than he bowled in this match," said Ganguly.
"He's a class act but like anyone he can have an off game.
"I want him to do well because he's a wicket taker...He has to bowl better than this if we are to be successful."
Ganguly said he was pleased by his team's overall performance in the first Test, which ended in an inevitable draw after the first three days were interrupted by rain but said the players would have to improve for the second Test starting in Adelaide on Friday.
"When you play against a good side like Australia you all have to perform...I think the bowling needs to be a bit better if we want to win test matches and we have to keep on getting 400 runs if we want to beat Australia.
"Cricket is a confidence game. All 22 who take the field in Adelaide will have to start from scratch and do well again."