The move came as Noshi Atta Girgis, fatally stabbed on Friday by a man officials said was mentally unstable, was to be buried. At least five others were wounded in the attacks on three churches.
The interior ministry said Mahmoud Abdul Razak Salah Eddin Hussein, 25, had been arrested.
Alexandria Judge Samy Breik ordered Abdul Razak to be held in custody for four days, charged with murder, illegal entry into a place of worship and illegal possession of weapons.
While the ministry spoke of only one assailant, police said there were in fact two attackers carrying knives and put the number of wounded at 12.
Witnesses said Abdul Razak shouted, "There is no god but Allah and Muhammad is the messenger of God," a statement that is one of the main tenets of Islam, as he carried out his attacks.
Egypt's Muslim Brotherhood in Alexandria denounced the attacks.
"We consider this crime an attack against all the Egyptian people, Muslim and Copt," a statement said, calling on security forces to protect places of worship.
It also warned against using the incident to "threaten the unity of the Egyptian people".
Egyptian Copts typically attend weekly Mass on Friday, which is also the Muslim holy day and marks the beginning of the weekend.
Copts make up about 10% of Egypt's mostly Muslim population of 73 million.
Men calm the son (C) of Noshi
Atta Girgis, who was killed Friday
Coptic faithful, religious leaders and intellectuals expressed fear of further harassment after the gains of the Muslim Brotherhood in parliamentary elections last autumn.
Muslim Brotherhood spokesman Issam al-Aryan expressed disbelief over the security forces' failure to prevent the attack.
"It's very sad news. I cannot understand what the security and police were doing. They are supposed to be guarding the churches," he said.
The deadliest recent communal clashes occurred in October, when Muslim protestors attacked a church in Alexandria that they said hosted a play they deemed offensive to Islam. Three people were killed in the fighting.
A 19-year-old Muslim who stabbed a nun during the rioting was sentenced to three years in jail in February.