The headquarters located in Azizabad neighbourhood was also the residence of MQM chief Altaf Hussain who fled Karachi in early 1990s and now lives in London as a British citizen.
Colonel Tahir of Rangers told media that the operation was launched at about 5.00 am and continued for two hours.
"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 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 also partially closed due to fear of violence.
There were reports that Rangers personnel after breaking barricades leading to MQM headquarters cordoned off the entire area and searched the party's offices. They also raided adjoining houses and arrested many MQM activists and leaders.
Prominent MQM leader Faisal Sabazwari in a hastily called press conference criticised the raid and asked Prime Minister Nawaz Sharif to intervene.
He said MQM was a peaceful party and was being targeted for its struggle for the oppressed Urdu-speaking people who migrated from India to Pakistan in 1947 during the partition.
MQM announced a day of peaceful protest against the search operation.
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