ATC Judge Raja Shahbaz Khan in Gilgit city sentenced the politician, living in London since 1992 on self-imposed exile, to 81 years imprisonment and also imposed a fine of Rs 2.4 million on him.
The judge ordered the Inspector General of Police of Sindh province to execute the court order as 62-year-old Hussain has permanent residence in Karachi.
The judge also ordered authorities to confiscate the properties of the MQM chief and open the same for auction.
Dozens of cases were registered against the MQM chief in in different cities of Pakistan on charges of treason, incitement to violence and speeches against the state and armed forces.
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The Lahore High Court (LHC) has already imposed a ban on media coverage of Hussain and airing of his images and speeches across all electronic and print media in a case.
The party has challenged the High Court's order in the Supreme Court.
MQM is a Karachi-based major political party of Urdu-speaking people who migrated after partition from India but it ran into troubles after Rangers and police launched operation in the city in 2013 to create peace with the backing of powerful army.
Hussian has been also facing charges of money-laundering in London.