"I support efforts of Egyptian civil and religious authorities who are in favour of a society that respects the rights of all people, particularly of minorities for the benefit of a unified nation," the pope said during a general audience in the Vatican.
Twenty-five Coptic Christians died and hundreds more were injured on Sunday during clashes with Egyptian soldiers and residents in Cairo. The Christians had originally gathered to protest against against the burning of a church.
Egypt's ruling military council has ordered a swift inquiry into the violence and the United Nations on Tuesday urged authorities to carry out an impartial and independent investigation of the bloodshed.
Copts, who make up about 10 percent of Egypt's 85 million population, have said they are not adequately protected by the country's military, which is in temporary charge of the country while elections are organised.
They say the authorities have been slow to punish radical Islamists who have attacked their churches in overwhelmingly Muslim Egypt, the Arab world's most populous country.
The military was handed the power to govern by former president Hosni Mubarak before he was toppled in the popular revolt earlier this year.
"I am deeply saddened by the episodes of violence that were committed in Cairo last Sunday. I share that pain of the victims' family's and of the entire Egyptian population," Benedict said, adding that minorities must be protected "above all in this moment of transition."
Egypt's Coptic Christians have on numerous occasions been on the receiving end of violence instigated by radical Muslims. The political vacuum left by the overthrow of Mubarak has prompted worries that mounting violence against Christians would be more tolerated than under the authoritarian government.