Homes and businesses have also been targeted, the Egyptian Initiative for Personal Rights (EIPR) says.
Witnesses described the attackers as shouting slogans in support of ousted Islamist President Mohammed Morsi.
But his Muslim Brotherhood supporters say it is the military regime that is instigating the violence.
Egypt's Christian minority is estimated to make up about 10% of the country's 85 million population.
According to the EIPR, at least
25 churches across Egypt were attacked by arsonists on Wednesday and
Thursday, following the violence in the capital, Cairo, between security
forces and supporters of Mr Morsi.
Christian schools, shops and homes were also targeted, it said.
The Mar Gergiss church in Sohag, a city about 390km (240
miles) south of Cairo, with a large community of Coptic Christians, was
Witnesses likened the area to a ghost town, with residents hiding indoors.
Patriarch Louis Sako, the head of the Chaldean Catholic
church which is based in Iraq, said churches belonging to his community
in Egypt were among those targeted on Wednesday.
"This is a real disaster," he told the AFP news agency, saying the region was a "dangerous volcano".
On Wednesday, hundreds of people were killed when the
security forces stormed two camps in the capital where the ousted
president's supporters had been demanding his reinstatement.
It is impossible to say whether the decision to break up the pro-Morsi camps in Cairo was the trigger for the church attacks.
But Egypt's minority religion has often borne the brunt of discrimination and violence from some Islamists.
The Muslim Brotherhood has accused Christians, particularly the Copts, of supporting the toppling of Mr Morsi.
The Coptic Pope Tawadros II appeared to back the military after it deposed Mr Morsi on 3 July following mass protests.
In turn, many Christians say Mr Morsi's government was deliberately squeezing religious pluralism.
The head of the army, Gen Abdul Fattah al-Sisi, has described the attacks as a "red line" and promised to respond forcefully.
Yet much of the violence has taken place outside urban areas, where there are few security personnel to intervene.