Abdel Magid Mahmud said in a statement that the three men were charged with premeditated murder aimed at harming national interests.
The suspects were arrested a day after the six Copts and a Muslim policeman were shot dead along a stretch of road with churches and a shopping centre in the southern village of Nagaa Hammadi.
The drive-by shooting took place after worshippers emerged from midnight mass before Christmas, marked by Copts and other Orthodox communities across the world on January 7.
The killings, which were condemned by Pope Benedict XVI, sparked outrage among the country's Copts, who make up nearly 10 percent of Egypt's 80 million people, and led to clashes with police.
A number of Muslim and Coptic homes and stores were attacked and burnt in the ensuing violence.
Italian Foreign Minister Franco Frattini, on a visit to Cairo on Saturday, expressed "satisfaction at the quick reaction of the Egyptian authorities and the arrests" of suspects in the killings.
Last week he condemned the violence against Copts as "horrific and outrageous," and said he would discuss "the protection of the Copt community" with Egyptian Foreign Minister Ahmed Abul Gheit in Cairo.
"The international community cannot remain indifferent and must never lower its guard in the face of religious intolerance, which is a serious violation of basic human rights," Frattini said on January 7.
After their meeting, Abul Gheit insisted "there are no clouds between" Italy and Egypt, despite Frattini's previous harsh criticism.
Sectarian clashes occur regularly in Egypt, particularly in the rural south, but this month's attack was the bloodiest since 20 Copts died in clashes in 2000.
Egyptian human rights activist Hafez Abu Saada said the trial would be the first conducted by a state security court over a sectarian attack. Such courts allow no right of appeal.
"It's a message of reassurance to the Copts and to affirm the government's concern towards this case," he said.
Copts complain of discrimination in Muslim-majority Egypt. They are permitted to build churches only after they get presidential permission and must apply to their governor to renovate churches.
The prosecutor did not announce a date for the trial.
Meanwhile, police released some 30 activists and bloggers who went to Nagaa Hammadi to express their solidarity with the families of the shooting victims, but they will still face charges, a blogger said.
Wael Abbas, a prominent opposition blogger among those arrested, said they were charged with belonging to an illegal organisation and trying to harm national unity, among several other charges.