The attack on the church in Atfeh, 100 kilometres from the capital, took place on Friday after weekly Muslim prayers, the diocese said on its Facebook page.
Several churches, especially ones that have yet to be licenced by the government, have come under attack by local Muslims in the conservative south of the country.
The diocese said the Prince Tawadros church had been used for almost 15 years and had applied for a licence under a law passed last year meant to ease permits for new churches.
"They stormed the place and destroyed what was inside it, after assaulting the Christians there," the diocese said.
Egypt's Coptic Christians comprise up to 10 percent of the country's 93 million people and are the Middle East's largest religious minority.
They have come under sectarian attacks and been targeted by jihadists who have killed more than 100 people in church bombings and shootings since last December.
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