The arrests followed President Gen Pervez Musharraf's pledge last week to eliminate religious extremism in Pakistan, Ahmed said.
Police raided mosques and homes and arrested "several dozen" Sunni clerics and activists for allegedly delivering hateful sermons against Shiites and distributing anti-Shiite pamphlets, Ahmed said.
Most Sunnis and Shiites live peacefully. But extremist Sunni and Shiite groups are blamed for attacking members of the other sect in violence that kills scores annually.
The detainees have not been formally charged. They face charges of misusing mosque loudspeakers or distributing literature containing sectarian material. If convicted, they could face six months to seven years in prison.
It was unclear when they would face court.
Following Musharraf's comments, prominent Shiite cleric Allama Hassan Turabi was killed in a suicide bombing Friday in the southern city of Karachi. His killing sparked massive riots by supporters.
About 80 per cent of Pakistan's 150 million people are Sunni, with Shiites comprising most of the remainder.