The police said the case was registered based on Pannun's social media video.
The Punjab Police has booked Gurpatwant Singh Pannun of the banned Sikhs for Justice on charges of promoting enmity between different groups on grounds of religion or race.
The FIR was registered at Amritsar's Sultanwind police station on January 23, the police said on Wednesday.
Pannun has been designated as a terrorist by the Union Home Ministry under the Unlawful Activities (Prevention) Act and the Sikhs for Justice banned.
In a video posted on social media, Pannun allegedly claimed that the Shri Durgiana Mandir in Amritsar had no historical significance in Hinduism.
The pro-Khalistan leader also purportedly warned the temple management to shut its gates and hand over the keys to the Golden Temple administration.
The police said the case was registered based on Pannun's social media video.
He has been booked under sections 153A (promoting enmity between different groups on grounds of religion, race), 153B (making or publishing statements that promote disharmony or hatred between different religious, racial, language, or regional groups) and 505 (whoever makes, publishes or circulates any statement, rumour or report) of the Indian Penal Code and provisions of the IT Act, the police said.
Pannun on January 16 issued a veiled threat to Punjab Chief Minister Bhagwant Mann and police chief Gaurav Yadav as he asked gangsters in the state to join the Sikhs For Justice and stop top political leaders from attending the Republic Day parade.
Pannun equated Punjab Director General Police Yadav to assassinated officer Gobind Ram, who was killed in a bomb blast in 1990.
In one of the purported videos, Pannun dared Prime Minister Narendra Modi to attend the Republic Day parade without security.
In another video, he asked gangsters in Punjab to join the Sikhs for Justice, participate in a referendum for Khalistan, and also prevent Mann from hoisting the Tricolour on Republic Day.
The email sent to journalists, however, deviated slightly from the videos where Pannun, besides giving a call to Punjab gangsters to join the Sikhs for Justice, also asked them to get recognised as "shaheeds (martyrs)".
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)