A church in the southern province of Minya was one of two shut down by local authorities.
A statement by the Coptic Orthodox diocese of Minya claimed worshippers were harassed at both churches and rocks were also throws at one of them.
It read: "We have kept quiet for two weeks after the closure of one of the churches, but due to our silence the situation has worsened ... it is as if prayer is a crime the Copts must be punished for."
Rumours of a pending attack forced a third church to close, according to Reuters, however the diocese confirmed no attack has taken place since but the church remains closed.
Coptic Christians, who comprise of approximately ten per cent of the country's population, have long complained of persecution.
Many feel the state does not take their plight seriously enough.
The diocese of Minya echoed this opinion.
Their statement added: "We have been trying to find any place to hold religious rites, while avoiding prohibitions against the (large) movements of the Copts, and potential dangers. Such places could be a hall, a house or even a simple room with poor ventilation. Even that is also prohibited.
"And although the constitution guarantees the right of worship, this right is in reality denied by the personal will of local officials. Often times, the matter has become akin to pursuing the Copts to prevent them from praying.
"In some instances, it has gone to the extent of using force against people and religious leaders."
"We are still waiting, and we will not despair. We published what happened as a reminder, may be the matter calls for the intervention of officials in Cairo, the capital."