Police opened fire Tuesday on unarmed Shia Muslim protesters in the northern city of Kaduna, leaving three dead, the spokesman for Shias in Nigeria said, as activists accused soldiers of having killed hundreds of Shias in "a massacre" in a nearby town in recent days.

Spokesman Ibrahim Musa of the Shia Islamic Movement in Nigeria says 10 people were also wounded when police shot "peaceful protesters." They were condemning the mass killings over the weekend and early Monday in the ancient Muslim university town of Zaria, and demanding the military release their leader, Ibraheem Zakzaky.

The bloodshed in Zaria was yet another blow to Africa's most populous nation, already beset by a six-year-old insurgency waged by Boko Haram, a violent Islamic extremist group which is at odds with the Shias and others who oppose its extremist views.

The police spokesman in Kaduna did not immediately respond to requests for information.

Musa said soldiers on Monday carried away about 200 bodies from around Zakzaky's home in Zaria, and hundreds more corpses are in the mortuary. Human rights activists said hundreds upon hundreds, perhaps as many as 1,000, have been killed.

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Activists say the Nigerian military staged raids over the weekend in the ancient Muslim town of Zaria. (CBC/Google)

The army said troops attacked sites in Zaria after 500 Shias blocked the convoy of Nigeria's army chief, and tried to kill him on Saturday. A report from the military police said some Shias were crawling through tall grass toward Gen. Tukur Buratai vehicle "with the intent to attack the vehicle with (a) petrol bomb" while others "suddenly resorted to firing gunshots from the direction of the mosque."

Ojo Momodu, a witness, said the Shias barricaded the road with burning tires as Buratai approached and then stoned his convoy. The group, however, denied that it blocked the road.

The military raids on Zakzaky's home and spiritual centres in two other areas in Zaria began hours later.

Chidi Odinkalu of the Nigerian Human Rights Commission called the attacks "a massacre." He posted photos on social media showing a bulldozer tearing apart a Shia shrine, but doubts later emerged about whether the image was actually from Zaria. He also said Zakzaky's home was destroyed.

Wife, sons reported killed

Odinkalu told The Associated Press that Zakzaky suffered four bullet wounds and one of his wives was killed in raids that began Saturday and ended Monday morning. He was quoting the family doctor.

Two of Zakzaky's sons also were killed and one was wounded, according to Musa.

Odinkalu and other human rights activists said there are hundreds of bodies at the mortuary of the Ahmadu Bello University Teaching Hospital on the outskirts of Zaria.

"Citizens must ask, who ordered this carnage?" Odinkalu tweeted.

Maj Gen. Adeniyi Oyebade, who was in charge of the military operation, told reporters Monday night that the military acted because they had reports the Shias were gathering for an attack. "Of course, because of the report I got that they are mobilizing, I had to order that the Gyallesu (Zakzaky's residence) and Huissaniya (shrine) be brought down," he said.

He said both the military and the Shias suffered casualties and that the dead were still being counted.