Without naming Khan, Rajnath Singh told the parliament that despite insults, iconic Dalit leader "BR Ambedkar never said he would leave India".
On Wednesday, the actor clarified that he had no intention of leaving India.
But several leaders of Mr Singh's BJP party have criticised him.
On the opening day of the winter session of the parliament, MPs began by paying tribute to Ambedkar - the independence hero who wrote India's constitution.
Ambedkar was a Dalit - formerly untouchables - who were socially discriminated against by India's higher castes.
"Dr BR Ambedkar had to put up with insults and derision. Yet, he controlled his emotion and put forward an objective point of view for India. He never said how he was being ignored and insulted in India," Mr Singh said in his remarks in the Lok Sabha, the lower house of the parliament.
"He said I will stay in India and keeping the Indian values and culture in mind, I will strengthen the country," Mr Singh added.
On Monday, actor, director and producer Khan told a journalism awards ceremony organised by The Indian Express newspaper that a sense of "insecurity" and "fear" had been growing in India.
He said he was "alarmed" over rising intolerance and his wife had even suggested leaving the country.
Following criticism from BJP politicians and several of his Bollywood colleagues, Khan on Wednesday put out a statement on his Facebook page saying he had never intended to leave India.
"Let me state categorically that neither I, nor my wife Kiran, have any intention of leaving the country. We never did, and nor would we like to in the future."
Despite his clarification, the controversy refuses to die down and the home minister's comments are seen as the latest salvo fired at him by BJP politicians.
Mr Singh's comments are also important as they were spoken in the parliament, where the government will later seek to push a key bill on a uniform countrywide goods and services tax.
The government wants to implement one of India's most significant tax reforms since Independence by April 2016.
However, the session is likely to be a stormy one, with opposition parties demanding a debate on "growing intolerance" in the country.
BJP leader Venkaiah Naidu said the government was "willing to discuss all issues, including the so-called issue of rising intolerance even though the incidents that happened were in the domain of statesâ€¦ We do not support or condone such incidents".
India's home minister has made remarks that are being seen as a jibe against Bollywood superstar Aamir Khan, for saying that his wife had suggested they leave India over growing "intolerance".