Residents in the province of Qena said four shops owned by Coptic Christians were torched overnight after villagers accused one of the store owners of molesting the young girl.
The clashes took place in the village of Marashda in Qena province.
Residents said protesters threw stones at the local church after midday Friday Islamic prayers. Police fired tear gas to scatter the crowd, which is in one of Egypt's poorest areas.
Qena security director Gen. Salah Mazid was quoted in state media saying that police are investigating the accusations against the merchant.
Flare-ups of violence between Egypt's Christians and Muslims have become more frequent in the past two years in the wake of the country's uprising that ousted longtime President Hosni Mubarak but also weakened security across the nation.
Egyptian Christians fear that the power vacuum that has followed Mubarak's overthrow is giving ultraconservatives and extremist Muslims a freer hand to attack churches and Coptic property, especially in poor areas of the nation.
Egypt's Coptic Christians, who make up about 10 percent of the country's 85 million people, have long complained of discrimination by the state. They are the largest Christian community in the Middle East.
Clashes between Copts and Muslims are usually sparked by church construction, land disputes or Muslim-Christian love affairs.