Raising the issue during Zero Hour, Raut said while the Home Ministry repeatedly said that ISIS had very limited influence in India, the "facts" coming to light suggest that poison was being spread among youth.
He claimed that 21 youths, including five women and three children, who had disappeared from Kerala had gone to Afghanistan and joined ISIS.
The cause of concern was that five among those who went to Afghanistan, had changed their religion.
Early last month, Naik had reportedly denied his involvement in the Dhaka attacks and called the Islamic State "un-Islamic".
Raut said the recent arrests from different parts of the country showed that ISIS has spread its network.
He also alleged that Jamaat-ul-Mujahideen had spread its network in parts of West Bengal and was targeting unemployed youths to join them.