Raut, who is a Rajya Sabha member and the executive editor of Shiv Sena mouthpiece 'Saamana', said the country cannot be run in a "Talibani" style.
After Padukone's visit to the Jawaharlal Nehru University (JNU) on Tuesday, many appreciated her "silent solidarity", but some others criticised her for "supporting Leftists", saying it was a promotional stunt for her latest film "Chhapaak".
Some also demanded a boycott of her film, based on the life of an acid attack survivor, played by Padukone.
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A section of BJP leaders also criticised the 34-year- old actor over her JNU visit.
Talking to PTI, Raut said, "The demand for boycott of the actress and her film is wrong. The country cannot be run in a 'Talibani' style."
"Chhapaak", directed by Meghna Gulzar, hit the theatres on Friday.
The Congress governments in Madhya Pradesh and Chhattisgarh on Thursday declared the film tax-free in the two states.
Declaring a movie tax-free means the state has waived the entertainment levy imposed on it, thereby bringing down the ticket rates and encouraging more people to watch it.