At least 12 people have been shot dead at a church in southeast Nigeria, with authorities suggesting the bloodshed was due to a local feud.

Witnesses said five gunmen stormed St Philip's church in Ozubulu, near the city of Onitsha, at 6am local time, and opened fire on worshippers.

The police, however, said the killing was the work of a lone attacker.

No one has claimed responsibility for the attack.

Garba Umar, the Anambra State police chief, said the violence was tied to a feud within the local community.

"The information at the disposal of the police is that the gunman had been hired to kill a particular family person believed to be among the worshippers," he said.

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Witnesses described chaos and bloody scenes at the church.

"I saw my fellow church members dead in a pool of their own blood and many others were screaming in pain," said Chukwuma Emeka who entered the church after the shooting.

A worker at the Nnamdi Azikwe University Teaching Hospital said 12 people have been confirmed dead, and many others with gunshot wounds were also receiving treatment there.

Local rights activist Emeka Umeagbalasi said his information about the motive largely concurred with that of the police version.

The gunmen went to the church looking for the son of a local chief, and opened fire on the parishioners when they could not find him, Umeagbalasi said.

Attacks on churches are rare in southern Nigeria, which is predominantly Christian.

Authorities said they do not believe that the armed group Boko Haram was behind the attack.

Boko Haram fighters have attacked hundreds of churches and mosques in Nigeria's mainly-Muslim north since 2009.

The rebellion has killed at least 20,000 people and forced some 2.6 million others to flee their homes, sparking a dire humanitarian crisis in the country's northeast.