An Aswat Masriya witness said on Friday that the police arrested six persons who threw petrol bombs and stones at Mar Girgis church in Aswan.
They also tried to storm into the church which caused the injury of three, one of them a police officer.
The clashed resumed on Friday afternoon between the police forces and protesters who accused the church of kidnapping a Muslim woman with the intention of converting her to Christianity.
The security forces threw teargas bombs to disperse the protesters.
The allegedly kidnapped woman is called Huda Tuni, aged 37.
Hundreds gathered in front of the church on Thursday after rumors spread that the woman was kidnapped to be forced into converting.
The church and the security forces denied that the girl is kidnapped for conversion, saying that it is a standard case of disappearance.
Archbishop Yohana Rizk stressed that finding the missing woman is the responsibility of both Muslims and Christians.