"If people are not provided protection, Pakistan will break into pieces. Christian, Barelvis, and Shias' will demand a separate state for themselves," warned London-based Hussain.
His comments came at a conference organised to promote harmony between different sects of Islam and other faiths.
Today unidentified gunmen targeted and killed seven Shias of the Hazara community in Quetta, the capital city of Baluchistan province which has been the worst hit by the sectarian violence in recent months.
Civil and human rights groups and other progressive minded political leaders have also expressed concern over the growing sectarian violence and the growing fear and insecurity among the non-Muslim minorities particularly the Hindu and Christian communities.
Hussain also urged religious scholars to take practical steps to end the ongoing sectarian strife in the country.
Criticising the political leadership for their lack of interest in providing protection to people, he said anti-Shia videos were being uploaded on youtube to ignite sectarianism.
Condemning the brutal murders of Shias in Lalusar, Gilgit, KP, Quetta and Balochistan in recent times, Hussain said the incidents highlighted growing religious intolerance in the country.
"Tell me about any other incident in which people were pulled out off a bus and killed after being verified as Shia," he asked.
The MQM represents the Urdu speaking population which migrated from India and has a strong hold in Pakistan's biggest city Karachi and is a coalition partner of the ruling government in the centre and Sindh province.
"If law enforcement agencies cannot do their jobs then let people protect themselves. People who are taking Shias off buses and killing them are not just murdering Shias, they are conspiring to murder Pakistan," Hussain added.
The MQM chief urged religious scholars to establish a forum to promote religious harmony in the country.
