Nearly two weeks after the incident, President Hosni Mubarak made indirect mention of the attack, calling on Muslims and Christians to unite, in statements carried by the state-owned Al-Ahram newspaper.
"We are one people. We are not fanatics because we are all children of this land and there is no difference between Egyptian Muslims, Christians and Jews," Mubarak said.
Mubarak urged Egyptians to "rally together so as not to give anyone a pretext to sow discord" rejecting "sectarian disputes and extremism especially as there are some abroad seeking to deepen rifts between Muslims and Christians."
Egyptian officials have denied a sectarian element in the attack, insisting it is a purely criminal act and have linked it to the the alleged rape of a Muslim girl by a Coptic man in the nearby village of Farshut last November.
"If it were an instant reaction (to the rape), why did it not happen earlier?," said political analyst Issandr al-Amrani.
While the events may have started with a criminal act, the fact that authorities refuse to recognise the sectarian element in events that followed is "absurd," Amrani said.
"One must recognise there are tensions between Christians and Muslims in Egypt. This tension is even more acute in the south," said Mustafa Kamel al-Sayyed, professor of political science at Cairo University.
The theory of a revenge killing does not hold because the three men charged with the Nagaa Hammadi killings are not members of the raped girl's family, said Sayyed, adding: "Why would they choose to shoot at Copts on their Christmas eve?"
Egypt's minister of state for parliamentary affairs, Mufid Shehab, said that the investigation into the attack revealed "no religious motivations."
For his part, parliament speaker Fathi Surur said "one isolated incident should not be taken as proof of a religious conflict."
But on Sunday, Coptic MP Georgette Qellini insisted the incident should be recognised as sectarian, prompting strong opposition from lawmakers of her own ruling National Democratic Party.
Amrani said that the position of the authorities was expected.
"It's their usual reaction in most cases," he said. "They have the feeling that talking about it will turn local crises into a national one. There is a fear of opening the debate on a national level," he added.
"I think the government wants to minimise the gravity of the situation, to reassure Egyptian, Arab and especially international public opinion," Sayyed said.
International condemnations poured in after the attack with the United States saying the incident showed "an atmosphere of intolerance" in Egypt.
Italian Foreign Minister Franco Frattini condemned the violence against Coptic Christians in Egypt as "horrific and outrageous" while Pope Benedict XVI said the attack has "caused indignation among many people."
Copts, who account for nearly 10 percent of Egypt's population of 80 million, are the Middle East's largest Christian community but complain of routine harassment and systematic discrimination and marginalisation.
Three Muslims were arrested two days after the attack and charged with premeditated murder. They will stand trial before an emergency security court next month.
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