Police only intervened after catching members of the mob damaging the CCTV cameras on the church wall and the gate.
This is not the first time the church in Sultan Basha, which is 150 miles (240 kilometres) south of Cairo, has been attacked.
In July a mob held demonstrations over three days, which led to the temporary closure of the Anba Karass church in the village.
A video of one of the mobs shows men appearing to throw things at the church as many others are heard shouting.
About five security forces arrive on the scene, but their presence doesn’t appear to calm tensions down.
Soon after the crowd begins to disperse but then it reconvenes again the church entrance.
The crowd then resumes hurling what sounds like angry abuse at the church.
A scuffle breaks out between two men who forcibly push each other while other men are holding canes and waving them.
The police are outnumbered, but they eventually calm tensions down.
After the most recent demonstration, villagers also uprooted crops and damaged irrigation pumps belonging to Christian villagers.
The church is currently unlicensed, but have applied for official legalisation of their status as they have met all their legal requirements, according to International Christian Concern.
The 2016 Law For The Building and Restoration of Churches says it is illegal to close down any unlicensed church that has officially applied for legislation.
It comes after another church in Egypt faced aggressive demonstrations from villagers that resulted in arrests.
The other village was Esna, which is about 433 miles (700 kilometres) south of Cairo.
The church, al-Zeneqia, had just finished worshipping and celebrating the Feast of the Assumption of the Holy Virgin.
An angry mob again was shouting they did not want a church in their village as the congregation was leaving after Mass.
Five demonstrateors were arrested as well as five Christians.