Naik, a notorious preacher, escaped India in 2016 and is wanted by Indian authorities on terror financing, hate speech, inciting communal hatred, and money laundering accusations.
The de-notification follows the dismissal of a no-confidence vote against Imran Khan by the deputy speaker of Pakistan's National Assembly.
According to education minister Dinesh Gunawardena, only President Gotabaya Rajapaksa and his elder brother, Prime Minister Mahinda Rajapaksa, will remain in their positions.