Demonstrators chased the state minister for economic development, Osman Mohammed 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.
There has been no early claim of responsibility for the bombing.
But Al-Qaeda has called for punishment of Egypt's Copts over charges that two priests' wives they say had converted to Islam were being held by the Coptic Church against their will.
A security official said on Sunday that about 20 people were detained for questioning but there was no evidence any of them was directly connected to the attack.
The bombing came two months after an Al-Qaeda affiliate claimed responsibility for a deadly Baghdad church raid which it said was aimed at forcing the release of the women in Egypt.
President Hosni Mubarak said Saturday's attack bore the hallmark of "foreign hands," and the interior ministry also blamed "foreign elements" -- indicating Islamist militants such as Al-Qaeda.
Mubarak pledged on television to "cut off the head of the snake, confront terrorism and defeat it" and urged Egypt's Christians and Muslims to unite in the face of a common enemy.
At least 5,000 people attended funerals late on Saturday for the victims at a monastery outside Alexandria, where crowds of mourners shouted slogans and refused to accept official condolences.
"No, no, no," the crowd shouted as a church official tried to read out condolences from Mubarak.
Government and independent newspapers warned on Sunday that "civil war" could break out in the country unless Muslims and its minority Christians close ranks.
They also urged the government to focus on the situation of the Copts, who account for up to 10 percent of Egypt's 80-million population and often complain of discrimination.
"Someone wants to make this country explode ... We must realise that there is a plot aimed at triggering religious civil war," the pro-government daily Rose El-Yussef said.
In the southern province of Assyut, a protest in the village of Al-Izziya on Sunday turned violent when Coptic demonstrators assaulted a Muslim and destroyed three cars, a witness said.
Saturday's bombing drew international condemnation, with Pope Benedict XVI urging world leaders to defend Christians against abuse and US President Barack Obama denouncing "this barbaric and heinous act."
However, Tayeb criticised Pope Benedict's call for world leaders to defend Christians as meddling in his country's affairs. The call amounted to "unacceptable interference in Egypt's affairs," he said.
French Prime Minister Francois Fillon on Sunday prayed for the victims at a church in the southern Egyptian city of Aswan where he was on a private visit, his office in Paris said.
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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.
There has been no early claim of responsibility for the bombing.
But Al-Qaeda has called for punishment of Egypt's Copts over charges that two priests' wives they say had converted to Islam were being held by the Coptic Church against their will.
A security official said on Sunday that about 20 people were detained for questioning but there was no evidence any of them was directly connected to the attack.
The bombing came two months after an Al-Qaeda affiliate claimed responsibility for a deadly Baghdad church raid which it said was aimed at forcing the release of the women in Egypt.
President Hosni Mubarak said Saturday's attack bore the hallmark of "foreign hands," and the interior ministry also blamed "foreign elements" -- indicating Islamist militants such as Al-Qaeda.
Mubarak pledged on television to "cut off the head of the snake, confront terrorism and defeat it" and urged Egypt's Christians and Muslims to unite in the face of a common enemy.
At least 5,000 people attended funerals late on Saturday for the victims at a monastery outside Alexandria, where crowds of mourners shouted slogans and refused to accept official condolences.
"No, no, no," the crowd shouted as a church official tried to read out condolences from Mubarak.
Government and independent newspapers warned on Sunday that "civil war" could break out in the country unless Muslims and its minority Christians close ranks.
They also urged the government to focus on the situation of the Copts, who account for up to 10 percent of Egypt's 80-million population and often complain of discrimination.
"Someone wants to make this country explode ... We must realise that there is a plot aimed at triggering religious civil war," the pro-government daily Rose El-Yussef said.
In the southern province of Assyut, a protest in the village of Al-Izziya on Sunday turned violent when Coptic demonstrators assaulted a Muslim and destroyed three cars, a witness said.
Saturday's bombing drew international condemnation, with Pope Benedict XVI urging world leaders to defend Christians against abuse and US President Barack Obama denouncing "this barbaric and heinous act."
However, Tayeb criticised Pope Benedict's call for world leaders to defend Christians as meddling in his country's affairs. The call amounted to "unacceptable interference in Egypt's affairs," he said.
French Prime Minister Francois Fillon on Sunday prayed for the victims at a church in the southern Egyptian city of Aswan where he was on a private visit, his office in Paris said.
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