It is understood an application to build the place of worship in El Toud near Luxor was abandoned after an angry mob targeted a site visit by local planning officials last week.
Crowds gathered in the village on Wednesday morning - chanting and throwing stones - as they voiced opposition to the plans.
Sami Farid, a Christian living in El Toud, told World Watch Monitor: "Many Muslim villagers gathered in front of the 'house church' and threw stones at it.
"They also pelted the Copt [Coptic Christian] homes next to the church.
"They shouted 'Allahu akbar' [Allah is the greatest], and chanted slogans against the church.
"Then they blocked access to the street leading to the church."
The situation did not de-escalate until one Christian denied to the visiting officials that they wanted to construct a new church building.
During a village meeting the following day, some Muslims also demanded that anyone trying to build a church in El Toud should be forced out of the area and their homes set on fire.
Home to around 500 Coptic Christians, believers in El Toud have been meeting since 2007 in the home of a church member.
The premise, which is used by a growing Christian population, is not officially recognised. Congregations seeking a church licence have experienced major difficulties.
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