The 50-year-old "PK" star during an award function in the national capital had said he has been "alarmed" by a number of incidents and his wife Kiran Rao even suggested that they should leave the country.
Mehra, who has directed Aamir in "Rang De Basanti", said he was in pain to hear the reaction against the actor for his comments.
"Aamir is a dear friend and I am in tears when somebody passes a comment because he is a true son of the soil for me. It is amazing. He does not have to prove anything," Mehra told PTI on the sidelines of IFFI.
"To all those people who are calling me anti-national, I would like to say that I am proud to be Indian, and I do not need anyone's permission nor endorsement for that. To all the people shouting obscenities at me for speaking my heart out, it saddens me to say you are only proving my point," Aamir had said in his statement.