Kher, 60, had earlier lashed out at Aamir for saying that he was "alarmed" by the rising intolerance in India.
"I don't have any problem with anybody. They all are my friends. Aamir is a friend too and we did a lot of films together like 'Dil', 'Dil Hai Ki Manta Nahin', but that time he wasn't 'Aamir Khan'. He then, rightly, over the years cultivated himself and became Aamir Khan.
"He then thought he should give opinions on everything... Whether it's the controversy of AIB, or whether it is this (intolerance) or that," Kher said.
The 60-year-old "Khosla Ka Ghosla!" star shared an incident from the 1991 film "Dil Hai Ki Manta Nahin", where Aamir had a problem with Kher's interpretation of his character.
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"(Mahesh) Bhatt sahab told me Aamir is saying your interpretation of your character is rubbish. This is not how he thought the character should be portrayed... So, sometimes people have this habit that they think what I am saying is right and rest of the world is not right."
Kher said he admires the work of the "Ghajini" actor, including his TV show "Satyamev Jayate", but feels a celebrity should be responsible.
Kher, whose wife Kirron is a BJP MP from Chandigarh, has not shied away from sharing his opinion on the issue of intolerance in public.
From criticising filmmakers returning their National Awards to leading a tolerance march in the national capital, Kher has shown his disapproval with stars like Aamir and Shah Rukh Khan, who have voiced their 'concern' over growing intolerance in the country.
"Everybody should speak, there is no treason, no anti-national issue. They are as patriotic as I am... It's very easy to portray me as a villain, who is opposing all these people. I am the same person who sat in Anna (Hazare) movement and stuck my neck out...
The "Special 26" star also criticised people like Yogi Adityanath and Sakshi Maharaj.
"They should be ashamed of making these statements. These are the people who are stopping the developing plan of BJP... I am never going to defend them," he said.