According to the Vicar-General of St Phillip's Parish in Baki Iku near the capital city Abuja, more than 200 attacked the church on Friday because it was holding a prayer meeting on the traditional day of prayer for Muslims.
Fr Luka Sylvester Gopep told This Day: "Sometime around 2pm, some Muslim youths in numbering 200 left their Mosque after their Friday Jumat prayer and rushed to the Church premises, climbed the wall and destroyed everything in the Church: the windows, the alter, musical instruments, the chapel.
"The security man in the church premises was beaten to pulp.
"Some women who were holding a prayer meeting were chased away. The seminarian who is resident in the premises was also beaten up and chased away."
He said an arrest had been made.
Niger State Police Command spokesman Bala Elkana told Vanguard that there were no casualties in the attack and police arrived quickly on the scene to stop violence escalating further.
The attack close to Abuja comes just a week after Muslim extremists murdered Mrs Eunicle Olawale, a travelling evangelist part of the Redeemed Christian Church of God, in the district of Kubwa.
Since President Muhammadu Buhari was elected into office in 2015 the Nigerian Army has made significant progress against Boko Haram - a jihadist group known for persecuting Christians.
However nomadic Muslim Fulani herdsman are still stealing land from Christians and last month it was reported they hacked a pastor to death.
The President, himself a Fulani, has condemned their actions and vowed to stop them, although Christians have criticised a bill currently being discussed by Nigerian politicians which could see the government buy swathes of land and give it to the herdsmen as permanent grazing and residential spots.
The Nigerian government has also closed down 70 churches in Lagos this year because of noise pollution, compared to 20 mosques and a dozen hotels, pubs and clubs.
