The case was registered by the Federal Investigation Agency (FIA) against London-based Hussain and other party leaders for their alleged involvement in the murder of former party leader Dr Imran Farooq, who was killed in the British capital in 2010.
An official of the FIA's counter-terrorism wing said the case was registered under section 7 of the Anti-Terrorism Act.
Besides the MQM chief, others charged in the case include Muhammad Anwar, Iftikhar Hussain, Moazzam Ali Khan and Khalid Shamim.
Farooq, a senior leader of the MQM who was also living in London in exile like Hussain, was stabbed and clubbed to death near his apartment in Green Lane, Edgware, in September 2010.
Farooq was ex-lawmaker, who according to various reports had fallen with the party chief and was contemplating setting up his own party before his murder.
The London Metropolitan Police has been investigating the case and their investigators had also came to Pakistan in July and September this year to interrogate suspects Moazzam Ali Khan, Khalid Shamim and Mohsin Ali, who are in custody of Pakistan's intelligence agencies.
The Pakistan government is still waiting for the London police to file a request for extradition of the three suspects.
Meanwhile, MQM denied the charges against the party chief and demanded justice in the case. It also demanded the arrest of killers of Imran Farooq.
MQM leader Khalid Maqbool Siddiqui said that it was an effort on the part of the government to "malign the party and its chief Altaf Hussain".
He fled Pakistan in 1992 and since then has lived in London. He is now a British citizen but still controls the party.
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.
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