Khadim Hussain Rizvi, chief of Tehreek-e-Labbaik Pakistan (TLP), and three other party leaders were charged on Saturday for making incendiary remarks against the judiciary and military chiefs after Aasia Bibi was acquitted of blasphemy by the Supreme Court.
"Today we have decided to take legal action against the TLP leadership," Pakistan's Information Minister Fawad Chaudhry told reporters.
"All those who were directly involved in destroying property, who misbehaved with women, who set fire to buses, are being charged under laws of terrorism at different police stations," he said, adding that more than 3,000 people had been arrested in connection with the TLP protests.
Rizvi, along with several other TLP leaders, was detained on November 24 after police launched a crackdown on hundreds of his supporters in Punjab province and the port city of Karachi.
Thousands of demonstrators, rallied by TLP, had blocked major roads, burning cars and buses last month, as they called for Bibi's execution to be carried out.
The chaos followed a landmark verdict which saw the Supreme Court overturn Bibi's death penalty and ordered her release after eight years in jail.
During the violent protests, one of the TLP co-founders, Afzal Qadri, called for mutiny against the powerful army chief, General Qamar Javed Bajwa, murder of the Supreme Court judges who acquitted Bibi, and branded Prime Minister Imran Khan as a "son of Jews".
Information Minister Chaudhry said Qadri was also charged with terrorism and sedition, along with senior TLP leaders Inyatul Haq Shah and Hafiz Farooqul Hassan.
"Sedition has a sentence of life imprisonment, they can face life imprisonment. All the charges will be submitted before the courts," Chaudhry said.
Saturday's move represents a hardening of the authorities' stance towards the group, which in late 2017 had also paralysed the capital, Islamabad, for several weeks and clashed with the police in deadly protests.
The TLP, whose main focus is protecting Pakistan's draconian blasphemy laws, had been calling for Bibi to be executed after she was acquitted.
Bibi, 53, was accused by two Muslim women of having insulted Prophet Muhammad and the Quran during an argument sparked by their refusal to drink water from the same vessel as her in 2009.
She was convicted and sentenced to death by a trial court in 2010, with the Lahore High Court upholding her conviction four years later. She was finally acquitted last month.
Bibi's husband, fearing for his family's safety, has pleaded for international help to leave the country.
Blasphemy against Islam and the prophet is a sensitive subject in Pakistan, where the crime carries a compulsory death sentence.
Increasingly, blasphemy accusations have resulted in mob lynchings and extrajudicial murders. An Al Jazeera tally says at least 74 such killings have taken place in Pakistan since 1990.