Flames were seen rising from the church, witnesses said. The Egyptian Foreign Ministry issued a statement condemning what it described as "assault," and that the church's priest was not inside and is unhurt.

Abdel-Salam al-Barghathi, a security official in Benghazi, said his forces stopped angry men from doing more damage to the church. He says they were angry about a protest by Christians in front of the Libyan embassy in Cairo, where they set fire to the Libyan flag.

The protests came after death of one Egyptian Christian detainee in Libya, whose family says he died of torture. They say Ezzat Atallah, who died in detention in Tripoli after being transferred from his prison in Benghazi, was one of around 100 Christians, mostly Egyptians, who were detained by militias on suspicion of trying to covert Muslims to Christianity.

Al-Barghathi appeared to blame the Christian protesters for the violence. He said Atallah died of natural causes and that he confessed before his death. "I got everything taped. He confessed and we videotaped his confessions. Why do the Christians burn the flag and replace it with a cross?" he said.

"These incidents will take place once and twice if the reactions on the other side continue like this," he warned.

Libya has seen multiple outbreaks of disorder since the 2011 civil war that led to the killing and ouster of dictator Moammar Gadhafi. The security and political vacuum has allowed hardline Islamist militias to act with impunity, especially since the government has relied on ex-rebel groups to keep order in absence of a functioning police force or a unified military.

On Sept. 11, four Americans including the U.S. Ambassador in Libya Chris Stevens were killed in an assault on the U.S. mission in Benghazi. An Islamist extremist militia that had been handling some security duties in the city, Ansar al-Shariah, was blamed for the attack. Months later, several Western countries withdrew their nationals from Benghazi citing imminent threats.

Churches, shrines used by traditionalist Muslims, and a Commonwealth war cemetery have also been vandalized in Benghazi and other cities in attacks blamed on hard-line Islamist puritans.

Last week, Egypt's Foreign Ministry intervened to win the release of 55 Egyptians who were in the group suspected of proselytizing. Thirty-five of them were deported for illegally entering the country, while 20 were cleared to stay in Libya.

Four foreigners under investigation for alleged espionage and proselytizing remain in a Libyan prison. They are a Swedish-American, a South Korean, a South African and an Egyptian.