The Deobandi and Barelvi groups clashed in Jani Burira village of Khairpur district when they took out rallies, local administration officials said.
"The participants of the Barelvi rally claim that some people in the Barelvi rally fired upon them at the Ameer Shah chowk," Senior Superintendent of Police Azfar Maheser said.
Sindh Home Minister Sohail Anwer Sial said that three persons were killed in the clashes. One more person succumbed during treatment.
He also directed Inspector General of Police (IGP) A D Khawaja to arrest the culprits.
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"Investigations show that activists of a banned outfit started the trouble as one of the suspects, who is also a wanted terrorist, questioned how the rallies were taken out without his permission," the police said.
The Sindh government has asked to shutdown mobile phone services tomorrow in Karachi, Hyderabad and Sukkur, the three major urban centres in the province to avoid any untoward incidents.
The two Sunni groups have deep theological differences but their armed fights are rare. Major conflicts erupt between Sunni and Shiite Muslims.
Yesterday, two worshippers were killed in Islamabad when a gunmen on a motorbike attacked a Shiite mosque.