"At present, we have a contractual agreement with creative agency Mc Cann Worldwide to produce social awareness campaign, which featured Aamir Khan," the ministry further clarified.
Incredible India is a government campaign to promote the country overseas.
The veteran actor was in the eye of a storm for his comments over growing intolerance in the country.
Later, he clarified that neither him nor his wife Kiran, have any intention of leaving the country as he is "proud to be an Indian".
"First 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. Anyone implying the opposite has either not seen my interview or is deliberately trying to distort what I have said. India is my country, I love it, I feel fortunate for being born here, and this is where I am staying," Khan said in a statement.
The brand ambassador of 'Incredible India' campaign also said that he is proud to be an Indian national and does not need anyone's permission to prove his Indianness.
"Secondly, I stand by everything that I have said in my interview. To all those people who are calling me anti-national, I would like to say that I am proud to be an Indian, and I do not need anyone's permission or endorsement for that," he said.
"To all the people shouting obscenities at me for speaking my heart out, it saddens me to say you are only proving my point," he added.
Khan also thanked people who stood by him and appealed to the people to protect India's integrity, diversity and inclusiveness.
"To all the people who have stood by me, thank you. We have to protect what this beautiful and unique country of ours really stands for. We have to protect its integrity, diversity, inclusiveness, its many languages, its culture, its history, its tolerance, it's concept of ekantavada, it's love, sensitivity and its emotional strength," he said.
He ended his statement with a poem by Rabindranath Tagore.
