The attack is the worst in a decade against the Egyptian Copt minority, which numbers around six million. According to international media reports, no one knows who perpetrated the attack and the government is pointing the finger at groups foreign to Egypt.
Many Copts took to the streets in protest.
Archbishop Michael Louis Fitzgerald, the Vatican's delegate to the North African nation, told Fides news agency that it was a moment to pray for peace and promote national unity, not one to perpetuate conflict.
The violence, however, was a sign to many that Egyptian Copts still are not receiving adequate protection from the government.
Pope Benedict deplored the New Year's killings, comparing them to the terrorist attacks carried out in Baghdad, Iraq in 2010 to intimidate Christians into leaving.
"This vile act of death ... offends God and all humanity, who only yesterday prayed for peace and began the New Year with hope," he said during the Angelus prayer in St. Peter's Square.
The Pope pointed out that this "strategy of violence" against Christians affects the entire population. His prayer was that that church communities would "persevere in faith" and bear witness to the Gospel message of non-violence.
In fact, the violence continued in Iraq during the Christmas season, as an Islamic extremist group made good on its threats to kill more Christians. On Dec. 29, terrorists killed two and wounded 20 in bomb attacks on Christian homes around Baghdad. The threats of violence had led to the cancellation of many Christmas celebrations in Iraq.
Despite the continued violence, Pope Benedict continues to hope for peace.
At Mass on Jan. 1, the 44th World Day for Peace, he encouraged prayers for the "fruitful conclusion" of efforts to achieve an end to war.
"In this difficult task words are not enough, we need concrete and constant commitment from the leaders of nations," he said. "But above all it is vital that everyone be animated by an authentic spirit of peace, which must be implored ever and anew in prayer and put into practice in daily life in all times and places."
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Following the Mass, he announced a coming summit of religious leaders for next October in Assisi, Italy.
The meeting will mark the 25th anniversary of the inaugural celebration of a similar initiative through which Pope John Paul II brought leaders from the gamut of religious traditions together to advocate peace in the world.
Pope Benedict called all people to support the cause through their prayers. He said, "those who are journeying towards God cannot fail to transmit peace, those who build peace cannot fail to move towards God."