Released after just 10 league appearances in his final season at City, 35-year-old Toure hit out at his former boss in a scathing interview with France Football.
Boateng was left bemused by the suggestions having encountered no such difficulties during the Catalan's successful three seasons at Bayern.
"I cannot share that opinion at all. I have never had a problem with him," Boateng said in an interview published by ESPN.
"On the contrary, I found as a coach he was super and that is why it is hard for me to comprehend."
Boateng is currently with the Germany squad preparing for the defence of their World Cup crown.
One player who will not be joining him in Russia is talented City youngster Leroy Sane, who was surprisingly omitted from Joachim Low's final 23-man squad.
Boateng praised the 22-year-old for the way he handled the news.
"He was very positive and has wished good luck to all of us," the Brazil 2014 champion said.
"Of course such a decision is difficult for a young player. But he has dealt quite well with it."