The "Kalicharan" actor's comment has come at a time when Aamir's comment on "despondency" and "disquiet" in the country, drew criticism.
Shatrughan tweeted: "I am fond of Aamir Khan and family. But wholeheartedly disapprove of the idea of India being labelled intolerant by him and others too. Our vast motherland is inherently and essentially peace loving and respectful of every caste, creed, religion and celebrates communal harmony."
The 69-year-old also said that the fact that Aamir's film "PK", which questioned religious discord and people's blind faith in godmen, was a success, shows there's tolerance.
"'PK', where Hindu gods and goddess were made fun of in no uncertain terms would not have seen such success if India was intolerant," he said.