The song, Besharam Rang was released on Monday, with Padukone and Khan moving to the beats at a beach in Spain.
Mishra was quoted as saying by the ANI news agency that the “costumes in the song at first glance are objectionable. It is clearly visible that the song of the film Pathaan has been shot with a dirty mindset."
He added, "I don't think this is right, and I will tell the director and makers of the film to fix it."
The minister also objected to the way "saffron and green have been worn, the colours of the song, the lyrics and the title of the film are not peaceful," saying, "it needs improvement."
He went on to add that they will "consider prompt action" if the film was not 'fixed' as suggested.