Angry Christian demonstrators pelted state minister for economic development, Osman Mohammed Osman with stones on Sunday, as fears rose of sectarian unrest after a bombing at a church that killed 21 people.
Hundreds of Coptic Christians gathered inside the gates of Cairo's St Mark's Cathedral where the Coptic pope, Shenouda III, has his headquarters and heckled officials who came to pay condolences.
Demonstrators chased Osman to his car and pelted him with stones after he met Shenouda, while others clashed with police standing outside the gates.
A police official said at least 40 policemen suffered light wounds when the protesters pelted them with stones.
More than a thousand protesters broke through the gates and spilled into nearby streets, stopping cars, banging on their hoods and pelting them with stones.
Earlier, dozens of protesters tried to surround the Imam of Al-Azhar, Ahmed al-Tayeb, Egypt's top Muslim cleric, and banged on his car after he went to see the pope.
Police officials also said more than 1,000 Copts demonstrated outside the foreign ministry and neighbouring state television buildings. Some protesters pelted passing traffic, damaging more cars.
It was the second consecutive day of such protests. On Saturday, Christian demonstrators heckled police and showered them with stones as they shouted slogans against the government.
At the Coptic church in the northern city of Alexandria that was targeted by an apparent suicide bomber, prayers were held on Sunday
"With our soul and our blood, we will redeem the Holy Cross," the grieving congregation chanted at the church of Al-Qiddissin during mass, just a day after the bombing.
Bloodstains from the attack were still visible on the facade of the church where 21 people were killed early on New Year's Day and 79 wounded.
Several hundred protesters also gathered outside the targeted church in Alexandria, but fanned into nearby streets and set fire to garbage bins after police prevented them from nearing the church.
The attack on Saturday in the Mediterranean city sparked angry street protests in Alexandria, with clashes between hundreds of Christian youths and police.