A MQM party worker was shot dead while several other party workers including a member of MQM's central coordination cell were detained during the raid, conducted by the Rangers, a paramilitary force.
The Rangers and the MQM share a thorny relationship and while the MQM had accused the Rangers of involvement in extra-judicial killings of its members, the Rangers had last month implicated the party in the Baldia Town factory inferno fire that claimed the lives of at least 258 factory workers.
"About 15 people have been taken into custody and prohibited weapons were recovered. We also found weapons stolen from NATO containers taking shipments from Karachi port to Afghanistan," he said.
"The arms that were seized during today's raid include many whose import is banned in Pakistan," a Rangers spokesman said, adding, several "hardened criminals and target killers" had been detained during the raid, including Faisal 'Mota' who had been awarded a death sentence for involvement in the murder of journalist Wali Khan Babar.
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Immediately after the raid, Hussain addressed workers from London on telephone and called for a day of mourning and peaceful protests.
He also blamed the Rangers for targeting the party and dismissed claims that large cache of arms or ammunition was recovered from the premises.
The MQM with Karachi as its stronghold went livid at the raid and hundreds of its workers arrived at the headquarters to protest. The city was closed due to fear of violence. Schools remained shut and examinations were postponed.