On Friday St Phillip's Church in Baki Iku, near the capital city Abuja, was ransacked by a group of Muslims unhappy that Christians were praying on the Islamic holy day.
Last week Muslim extremists murdered Eunicle Olawale, a travelling evangelist part of the Redeemed Christian Church of God, in the district of Kubwa.
In the biggest city Lagos, 70 churches have been closed down by the government citing concerns about noise.
Politicians are trying to wipe-out noise pollution by 2020 by in contrast has only closed 20 mosques and a dozen pubs, hotels and clubs.
In June one person was killed after churches and homes were set on fire during an attack in the southern Kaduna State.
Radical Islam is being blamed for all the attacks.
Tanya Corbett from anti persecution charity Open Doors told Premier's News Hour it was very worrying.
She said: "Attacks seem to be happening more frequently and they seem to be increasingly severe and very violent.
"It's a pattern that's emerging across Sub Saharan Africa where there is an increase in Islamisation.
"The threat and the fear of persecution is used to intimidate people and to drive people out of villages and communities.
"Obviously horrific attacks like these mean people are even more scared, even more fearful."
Open Doors said the problem could be much worse than is reported. Cases of persecution against Christians could be as much as 50 per cent higher than figures suggest, the charity said.
