Dan Manjang, an adviser to the government of Plateau State, where the attacks took place, said 95 arrests had been made.
Nigerian media also reported that Jonathan Goodluck, the country's acting president, had sacked Sarki Muktar, the national security adviser, on Tuesday.
However, it was not clear whether the sacking was linked to the latest sectarian violence.
At least two other villages near Dogo Nahawa were also targeted on Sunday in an area close to where sectarian clashes killed hundreds of people in January.
Al Jazeera's Yvonne Ndege, reporting from Jos, said the government had confirmed Sunday's death toll at more than 500 and had launched a huge security operation in an attempt to stop the violence from spreading to other states.
Our correspondent quoted police as saying that the attackers were Muslim Hausa-Fulani herders while the victims were mainly Christians from the Borom community.
Test for Jonathan
But she added that while many people would view the violence in a religious context, people she had spoken to said the violence was about indigenous groups, who are mainly Christian, and migrants and settlers, mainly from the Hausa-speaking Muslim north, competing for access to resources.
|Attacks occurred in three villages
south of Jos [AFP]
The latest violence in the centre of Africa's most populous nation comes at a time of uncertainty for the country, with Jonathan trying to assert his authority while Umaru Yar'Adua, the president, remains too sick to govern.
The situation is a test of Jonathan's ability to show that he has the power to deploy the police and army as commander-in-chief, and many people will be watching to see how he deals with the situation, our correspondent said.
In a statement after Sunday's attack, Jonathan's office said he had "directed that the security services undertake strategic initiatives to confront and defeat these roving bands of killers".
Gregory Yenlong, Plateau State's Commissioner for Information, said that "soldiers are patrolling and everywhere remains calm", but security officials have been criticised for failing to prevent another outburst of violence just weeks after hundreds died in Muslim-Christian clashes.
The violence appeared to be reprisal attacks following the January unrest in Jos when most of the victims were Muslims, Robin Waubo, a Red Cross spokesman, said.