The attacks on worshippers marking Palm Sunday in the Nile Delta cities of Tanta and Alexandria have been claimed by Islamic State.
President Abdel Fattah al Sisi said the state of emergency would be introduced after legal measures were taken.
He did not explain what those measures were but parliament must vote in favour before it is brought in, according to the country’s constitution.
The leader said: “Egyptians have foiled plots and efforts by countries and fascist, terrorist organisations that tried to control Egypt.”
The first explosion in Tanta, about 70 miles north of Cairo, killed at least 27 people and injured 78 at the Mar Girgis Coptic Church.
Officials said the blast happened “in the front rows, near the altar, during the mass”.
Video and pictures showed crowds gathered around bodies and large blood stains on the pews and church walls.
Several hours later, in the coastal city of Alexandria, a suicide bomber detonated his device in front of Saint Mark’s Church when police stopped him from storming the entrance.
At least 17 people died and 48 were injured.
Pope Tawadros II, head of the Coptic church, had earlier attended mass at the church.
Islamic State claimed responsibility for both bombings through its Amaq news agency.
Egypt is home to around nine million Coptic Christians, who have seen attacks on them increase in recent years.
Supporters of the country’s deposed Islamist leader, Mohamed Morsi, accused the Christians of supporting his overthrow in 2013.
A bomb at a Cairo cathedral that killed at least 25 people in December 2016, many of them women and children, was also claimed by IS.
Targeted killings in the country’s Sinai peninsula also caused hundreds of Christians to flee the area in February, with an IS video urging more attacks.
Pope Francis, due to visit Egypt at the end of this month, sent his “deep condolences” to the “dear Egyptian nation” and his “beloved brother” Pope Tawadros II.
Coptic churches also often suffer vandalism or arson, and Copts say they are sidelined from many posts in the police, justice system and universities.