Ayo Oritsejafor, head of the Christian Association of Nigeria, also said after a meeting of church leaders on Saturday that Christians would defend themselves, though he added that he was not advocating reprisal attacks.
The stark warning in Africa’s most populous nation and largest oil producer comes with at least six gun and bomb attacks targeting Christians since Christmas having killed more than 80 people.
Attacks have seen victims gunned down while their eyes were closed in prayer in church, caught up in a gruesome bomb blast while leaving Christmas services and shot while gathering to mourn the death of a friend.
In the latest violence, residents said gunmen shot dead three people believed to be Christians as they were playing poker on Saturday night in the northeastern town of Biu.
Islamist group Boko Haram has claimed most of the violence, which has sparked fears of a wider religious conflict in a country whose 160 million population is roughly divided between a mainly Muslim north and predominantly Christian south.
A purported spokesman for the group a week ago gave southerners living in the north a three-day ultimatum to leave the region. In claiming subsequent attacks, the spokesman said they were in response to the ultimatum.
At mass on Sunday in the capital Abuja, worshippers were frisked and made to pass through metal detectors upon entry — measures that have been in place for several weeks.
In the economic capital Lagos, which has not been hit by attacks, churchgoers were told to be on alert for any suspicious movements.
Oritsejafor said an emergency meeting of church heads concluded “that the pattern of these killings does suggest to us a systematic ethnic and religious cleansing.”
“We are reminded by the occurrences of these killings of the genesis of the civil war that took place here in Nigeria,” he added, reading from a statement prepared after the meeting in Abuja.
The run-up to Nigeria’s 1967-70 civil war that left more than a million dead saw Igbos, who are overwhelmingly Christian, massacred in the country’s north.
An attack Friday in the northeastern town of Mubi was a frightening reminder for many of the pre-civil war days, with 17 people gunned down as they gathered to mourn the death of an Igbo killed the night before.
Boko Haram has been blamed for intensifying violence for months, but it has taken on a different dimension with recent attacks targeting churches and Christians.
Bombings on Christmas, particularly one that killed 44 people as services were ending at a Catholic church near Abuja, sparked intense fear and outrage.
Under mounting pressure to act, President Goodluck Jonathan on December 31 placed areas hard hit by attacks blamed on Boko Haram under a state of emergency, but the violence has only continued and expanded into other locations.
In a televised address to the nation on Saturday evening devoted to a controversial policy that has seen fuel prices skyrocket, Jonathan spoke briefly of the violence, saying the “mindless acts of violence … are unfortunate.”
A number of the recent attacks, including in Mubi and in the cities of Yola and Gombe, have occurred in areas outside the emergency decree.
Officials in Adamawa state, the scene of most of Friday’s bloodshed and where Yola and Mubi are located, announced a 24-hour curfew on Saturday and deployed security forces in a bid to halt the carnage.
Boko Haram is a shadowy group believed to have a number of factions with differing aims, including a hard-core Islamist wing and those with political links.
It launched an uprising in 2009 that was put down by a brutal military assault in which some 800 people were killed.
Since the group re-emerged in 2010, it has been blamed — and often claimed responsibility — for increasingly sophisticated and deadly attacks, including the August suicide bombing of UN headquarters in Abuja that killed 25.