Mr Khan said he was "alarmed" over the rise of acts of intolerance in India and that his filmmaker wife Kiran Rao had even suggested leaving the country.
The BJP said Mr Khan should not forget that "India made you star" and it was incorrect to "malign Incredible India".
The party was referring to a TV campaign by Mr Khan to promote tourism.
Actor, director and producer Khan told a journalism awards ceremony organised by The Indian Express newspaper on Monday that a sense of "insecurity" and "fear" had been growing in India.
He said his wife had asked him whether the family should move out of India.
BJP spokesperson Shahnawaz Hussain criticised Khan's remarks and said there was a "political conspiracy to defame India" and there was "no better neighbour than a Hindu for a Muslim".
India's junior minister for home Kiren Rijiju said incidents of religious violence had come down since the BJP government, led by Narendra Modi, came to power last year.
"Mr Khan's comments on intolerance are misplaced. Comments like this only bring the image of the country and the prime minister down," Mr Rijiju was quoted as saying by The Indian Express newspaper.
Another BJP spokesperson, Sambit Patra, said that "Aamir Khan is the face of 'Incredible India', how can he make such a remark? I request Aamir Khan not to leave India and he won't find another nation like it".
Actor and BJP MP Manoj Tiwari said "it is unfortunate that Aamir Khan says intolerance is on the rise in India".
Khan's remarks have come after protests from fellow actors, writers and scientists over cases of intolerance.
Earlier this month fellow superstar Shah Rukh Khan also spoke out against what he called "extreme intolerance" in India.
A movement that began with writers returning state awards has spread to scientists, historians and filmmakers.
They have cited the killing of rationalists MM Kalburgi and Govind Pansare, as well as the lynching of a man over suspicions he consumed beef, as examples of rising intolerance in the country.
Earlier this month nearly 200 figures including author Salman Rushdie signed an open letter urging British Prime Minister David Cameron to raise "the rising climate of fear" in India with Mr Modi during his recent London visit.
However, Aamir Khan's comments have found opposition support, with Congress leader Rahul Gandhi taking the lead.
Mr Gandhi said "instead of branding those who question government and Mr Modi as unpatriotic, the government would do better to reach out".