His outrage on Twitter came as tensions simmered between the two countries over the divided Himalayan region after New Delhi last week rescinded years of autonomy enjoyed by the Indian-ruled part of Kashmir and gave full control to the central government.
Kashmir has been under virtual lockdown since shortly before the move, with a curfew across the region, and phone and internet lines cut -- ostensibly to prevent unrest.
Huge numbers of troops are patrolling the streets of major centres, and security forces used tear gas Friday to break up a demonstration by about 8,000 people against the government's move.
Kashmir has been split between India and Pakistan since their independence in 1947.
They have fought two wars over the former kingdom, while an insurgency against New Delhi's rule in Indian-administered Kashmir has claimed tens of thousands of lives in the past three decades.
Khan tweeted that the "ideology of Hindu Supremacy, like the Nazi Aryan Supremacy, will not stop" in Kashmir.
Describing the move as "the Hindu Supremacists version of Hitler's Lebensraum", he said it would lead to "the suppression of Muslims in India & eventually lead to targeting of Pakistan".
"Attempt is to change demography of Kashmir through ethnic cleansing," he tweeted. "Question is: Will the world watch & appease as they did Hitler at Munich?"
Indian Prime Minister Narendra Modi insisted last week the decision to strip Kashmir of its autonomy was necessary for its economic development and also to stop "terrorism".
He said with Kashmir now fully part of the Indian union, the region would enjoy more jobs and less corruption and red-tape, adding key infrastructure projects would be expedited.
Previously, under its constitutional autonomy, Kashmiris enjoyed special privileges such as the sole right to own land and take government jobs or university scholarships.
Islamabad has been infuriated by New Delhi's moves and has expelled the Indian ambassador, halted what little bilateral trade exists and suspended cross-border transport services.