A public inquiry on Monday accused the Nigerian army of killing 347 Shia Muslims and dumping them in a mass grave in the northern city of Kaduna late last year.

Two days of violence began on December 12 when Shia worshippers attending a religious ceremony obstructed the convoy of Nigeria's chief of army staff, Lieutenant General Tukur Yusuf Buratai.

"The Nigerian Army used excessive force," said the 193-page report, which is available online.

In total 349 people were killed including one soldier and one Shia worshipper who died later in custody.

The commission, setup by the Kaduna state government, said those responsible for the killings should be prosecuted, confirming the conclusions of an earlier Amnesty International report.

"The Commission therefore recommends that steps should immediately be taken to identify the members of the NA (Nigerian Army) who participated in the killings ... with a view to prosecuting them," it said.

'Nigeria should release el-Zakzaky'

Amnesty International accused the army of deliberately shooting dead the Shia followers of pro-Iranian cleric Ibrahim el-Zakzaky, burying them in mass graves and destroying evidence of the crime.

The military maintains that its soldiers acted according to the rules of engagement after the crowd attempted to assassinate Buratai.

READ MORE: Nigeria's Shia detainees 'dying' without medical care El-Zakzaky, who lost an eye and was left partly paralysed in the violence, has been held since December.

He has previously run up against Nigeria's secular authorities and has been imprisoned for calling for an Iranian-style revolution to create an Islamic state in the country's north.

"Political and military authorities in Nigeria should heed the Commission's recommendations and take immediate steps to hold those responsible for the illegal use of lethal force to account and to pay compensation to the victims," said Mausi Segun, Nigeria researcher at Human Rights Watch.

"The authorities should release el-Zakzaky and [his wife] Zeenah from detention, or bring credible charges against the couple in a properly constituted court."