The 28 members, including central leader Aamir Khan, were arrested by the Rangers from the central headquarters of the MQM, the main political party in Karachi, during a pre-dawn raid which led to Pakistan's biggest city Karachi shutting down.
The situation in the city remained tense today as Khan and the other arrested activists were brought blindfolded and handcuffed to the court amidst a large contingent of police and paramilitary Rangers.
Khan waved a V-for-victory sign as he was jostled on his way out from the court.
During the raid at MQM headquarters, a party party worker was shot dead, sparking an angry response from the party, with workers shutting down large parts of Pakistan's commercial hub.
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During the raid, security forces also seized a "huge quantity" of weapons and arrested activists, including one accused of murdering a journalist.
"The MQM maintains that Waqas Ali Shah was killed by Rangers personnel and we have enough evidence to prove this," said MQM leader Farooq Sattar.
Another MQM leader, Haider Abbas Rizvi lashed out at the Pakistan Tehreek-i-Insaf and its chairman Imran Khan for "celebrating" the raid.
He alleged that the "some political parties are seeing this as an opportunity to suppress MQM but their nefarious dreams will never come true".
The Rangers claimed recovery of a large cache of weapons and ammunition, but Rizvi said all of them were licensed.
The rangers and police have been carrying out a clean-up operation in Karachi since October 2013.