The demonstrations by the Gonabadi Sufi order, known as dervishes, turned into running clashes with the police in northern Tehran on Monday.
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Footage on state television showed a bus ploughing into a group of policemen in northern Tehran, which police said led to three deaths.
On Tuesday, police spokesman Saeed Montazer Almehdi said two members of the hardline Basij militia, which is linked to the Revolutionary Guards, were also killed.
"Two of our dear Basijis were martyred by the superstitious cult," he told the semi-official ISNA news agency.
Montazer Almehdi said "more than 300" people had been arrested, including the driver of the bus.
The Gonabadis, one of the country's largest Sufi sects, accuse the Iranian state of frequent harassment and discrimination.
Sufism is an accepted branch of Islam in Iran, but the practice is frowned upon by many conservative clerics. Officials and the media routinely refer to them as "deceived elements" or a cult.
Montazer Almehdi said police had struggled to talk the protesters down from the roofs of houses and that the protests had not been brought under control until late into the night.
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"Thirty police officers on the scene were wounded," he told ISNA. "A number of rioters were also wounded last night."
A website linked to the group indicated the protests were linked to the recent arrest of members of the sect and police efforts to establish security check points near the home of their leader, Noor Ali
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