The 57-year-old claims that not selecting the right players and being "too stubborn" could have a negative impact on Dhoni's future after the World Twenty20.
"I don't like to comment on internal matters of Indian cricket but it is a fact that I don't see a very good future for Dhoni after this ICC World Twenty20," said Qadir. "There is definite politics and problems within the Indian team.
"There is no way that you cannot play [Virender] Sehwag in the T20 form of cricket. He is a one-man army on his day and very destructive not playing him tells me something is wrong in the Indian camp.
"At times I feel that Dhoni is too stubborn in selection matters and it hurts their team. Opening with Irfan Pathan when you have far better options available is hardly intelligent cricket."
Pakistan and India will play each other in the Super Eights on Sunday.