The suspects, who were arrested after the attack, were charged with "premeditated murder, putting the life of citizens in danger and damage to public and private property," a judicial source said.
Al Jazeera's Amr El-Kahky, reporting from the Egyptian city of Luxor, said the court later announced it had adjourned until March 20 to allow defence lawyers time to read through case documents and come up with their requests.
"The accused have insisted that they have done nothing wrong and that they did not do that drive-by shooting. If that's right, that will arouse questions on who is behind the attack on Egypt's Christian minority here," he said.
"The judge that is overseeing this trial is one [who] belongs to a specially designed court that is designed to look into sectarianism.
"By so doing, the government is trying to send a message that it is not complacent and it is not collaborating with the perpetrators of this violent attack on the Egyptian Christian minority."
The killings sparked outrage among the country's Copts and led to clashes with police as Nagaa Hammadi residents accused the authorities of refusing to recognise the attack as sectarian.
Egyptian officials insisted it was a purely criminal act and linked it to the alleged rape of a Muslim girl by a Coptic man in November.
There has also been international condemnation of the attack, with the US saying it showed "an atmosphere of intolerance" in Egypt. Pope Benedict XVI said the attack "caused indignation among many people."
It was the deadliest attack since 2000, when 20 Copts were killed in sectarian clashes.