A 24-hour curfew was in place in the city on Wednesday but gunfire could be heard in neighbouring areas in Plateau state.
"The fighting has stopped in Jos, but we can hear gunshots in other communities in the outskirts of the city," Muhammad Tanko Shittu, a senior mosque official organising mass burials, said.
More than 150 citizens have died in the fighting, according to a mosque official, and streets have been left deserted and businesses closed.
"We are expecting more corpses to be brought in from surrounding communities later today," Shittu said.
The government said that only 20 people had been killed in the fighting, with 40 more injured, while leaders of both sides said nearly 300 people have died.Human Rights Watch (HRW), the international rights watchdog, called for the Nigerian military to show restraint as the government ordered additional soldiers onto the streets of Jos, the state capital, to keep control.
"Nigeria should ensure that its security forces use restraint and comply with international standards on the use of force in responding to the latest deadly outbreak of inter-communal violence," HRW said.
Charles Dokubo, from the Nigerian Institute of International Affairs, told Al Jazeera: "There is more than the religious aspect of it. There are two communities - one that call themselves settlers and one that call themselves indigenous communities.
"The crisis in the north started with the creation a local government."
Dokubo said that Muslim settlers were to manage the government, which was unacceptable to the indigenous Christian community who consider them non-citizens.
"The main cause of the crisis is about administration and the place where people belong."
Dokubo said that disputes over jobs may also be contributing to tensions between the two groups, with indigenous peoples' fears that settlers in government would give jobs only to other settlers.
The fighting erupted on Sunday in a Christian area due to a dispute over the building of a mosque, residents said.
Jos, which is home to 500,000 people, along with other central and northern areas in Nigeria have been plagued by religious violence in recent years.
In November 2008, hundreds of people were killed in Jos in two days of fighting triggered by a rumour that the mainly Muslim All Nigerian Peoples Party had lost a local election to the Christian dominated Peoples Democratic Party.
Nigeria has roughly equal numbers of Christians and Muslims, although traditional animist beliefs underpin many people's faiths.
More than 200 ethnic groups generally live peacefully side by side in the West African country, although one million people were killed in a civil war between 1967 and 1970 and there have been outbreaks of religious unrest since then.