The Islamic Movement in Nigeria (IMN), said 12 of its members were killed in a nationwide crackdown on Tuesday.
But the Nigerian police denied the claim, saying their men never killed any Shiite member.
The Shiites embarked on their annual religious rite, Ashura, across many states in Nigeria.
The group’s spokesperson, Ibrahim Musa, in a statement Tuesday afternoon said the killings took place after attacks on Ashura mourners in Kaduna, Bauchi, Sokoto and Katsina states.
The statement, however, said similar processions in Abuja, Jos, Kebbi, Minna, Lafia, Yola, Gusau, Zaria, Kano, Jalingo, Damaturu, Hadejia and Potiskum, ended peacefully.
Ashura, a Shiite mourning period in commemoration of the killing of Imam Hussein, a grandson of Prophet Muhammad, is observed on the 10th day of the first month of Islamic lunar calendar, Muharram.
The police had said in a statement on Tuesday that it would treat the planned procession as “a gathering in advancement of terrorism”.
The police’s warning on the Ashura gathering followed the proscription of the IMN by the Nigerian government and its designation as a terrorist organisation.
At least three people were confirmed killed by the police in Kaduna and 10 others injured, some fatally, when thousands of Muslim brothers and sisters trooped out in the early hours of Tuesday commemorating the tragic events of Ashura.
In Bauchi, reports also have it that three people were killed during the procession when the police attacked the mourners. Likewise three other people were killed by the police in Azare, also in Bauchi state.
Another 3 three people were reportedly killed by the police in Gombe, Gombe state.
One person was reportedly killed by the police in Illela and another person was killed in Goronyo all in Sokoto state.
In Malumfashi, Katsina State also another person was killed. In Katsina town, however, several people sustained bullet wounds when the police opened fire on the mourners, not only during the mourning procession but afterwards as the well-armed policemen attempted to forcibly make their way into the Islamic centre of the Movement.
These casualty figures may, however, rise due to the fatal gunshot wounds sustained by some of the peaceful mourners.
This year’s Ashura procession was held in all the state capitals of the North and Abuja. It ended peacefully in Abuja, Jos, Kebbi, Minna, Lafia, Yola, Gusau, Zaria, Kano, Jalingo, Damaturu, Hadejia and Potiskum.