Egypt's President Abdel-Fattah el-Sisi will attend a state funeral on Monday for the 24 Christians killed as they worshipped on Sunday.
The Copts were killed by a 22-year-old suicide bomber, Sisi said on Monday, adding security forces had arrested three men and a woman.
A private service conducted by Coptic Pope Tawadros II was held early on Monday for the relatives of those who died. Buses will then transport the coffins and immediate family to the state funeral attended by Sisi and other officials at the start of three days of national mourning declared by the President.
The attack on the spiritual home of Egypt's Coptic community, which make up 10 per cent of the population, was the worst on Christians in years.
Pope Tawadros cut short a visit to Greece to come back and take the services.
Before the service he said: "This calamity is not against the church but against the homeland, [against] all of Egypt.
"We are in a lot pain because of this evil.. but we are pleased they passed away during prayers, this is the best time to die.. during this [holy] month."
He added: "Whoever did this attack does not belong to the Egyptian people."
Pope Francis called the Coptic Patriach on Monday morning before the funeral to express to condolences and his closeness to the Coptic community.
"We are united in the blood of our martyrs," said the Catholic pontiff.
No group has claimed responsibility for the attack but Muslim Brotherhood leaders, who have been accused of waging a "witch-hunt" against Copts, condemned the attack. ISIS supporters have celebrated the killings on social media.
The bombing sparked waves of anger across Egypt with hundreds protesting outside the cathedral in Cairo.
The crowd demanded Magdy Abdel Ghaffar, the interior minister, be dismissed after a perceived security failure led to the attack. Christians are convinced attacks on them are not seriously investigated.
"The Ministry of Interior cannot protect our churches. It is time for us to protect ourselves," said one protester. Others demanded the fall of the regime.
Egypt's Christian community has felt increasingly insecure since Islamic State spread through Iraq and Syria in 2014, ruthlessly targeting religious minorities. In 2015, 21 Egyptian Christians working in Libya were killed by Islamic State.
