The first blast took place in the Coptic church of Mar Girgis, also known as St George, in the Nile delta city of Tanta, about 120 kilometres from Cairo, killing 25 people and injuring 71, according to a statement by the Health Ministry.
Security sources said the primary investigations suggest that a person put an explosive device inside the church during the Christian prayers celebrating the Palm Sunday. However, others said the attack was carried out by a suicide bomber.
The explosion targeted the front rows in the church hall. Among those killed is Samuel George, the head of Tanta Court.
Hours later, a suicide bomber struck the Saint Mark's Coptic Orthodox Cathedral in Alexandria's Manshyia district, police said.
At least 11 people, including police personnel, were killed while 66 others injured in Alexandria's suicide bomb attack, according to a statement by the Health Ministry.
In a statement, Interior ministry said a suicide bomber had planned to blow up himself using an explosive belt inside the church in Alexandria, but the security forces stopped him.
A police officer and a policewoman, as well a low-ranking police officer, were killed while preventing the suicide bomber from entering the cathedral, the ministry said.
It said Pope Tawadros II was inside the cathedral leading Palm Sunday Mass, but he was not harmed in the attack.
The Islamic State claimed responsibility for the attacks.
"Islamic State squads carried out the attacks on two churches in Tanta and Alexandria," said the group's propaganda news agency Amaq on its social media accounts.
Meanwhile, security forces have dismantled two explosive devices at Sidi Abdel Rahim Mosque in Tanta city. The mosque, which includes a Sufi shrine, is considered the second most important mosque in city, Al-Ahram Arabic reported.
President Abdel Fattah el-Sisi called for a National Defence Council meeting in response to the attack.
The National Defence Council is made up of the prime minister, the speaker of parliament, the minister of defence and the commanders of the Egyptian armed forces, and is chaired by the president.
President El-Sisi ordered the opening of military hospitals to receive the injured.
Al-Azhar, the world's highest seat of Sunni Islamic learning, strongly condemned the attacks, calling it an "outrageous crime" against all Egyptians.
"This terrorist attack is devoid of all the principles of humanity and civilisation," it said in a statement.
Al-Azhar Grand Imam Ahmed El-Tayyeb stressed Al-Azhar's solidarity with the Egyptian Church in the wake of attacks.
The US Embassy in Egypt condemned "the heinous, reprehensible terrorist attack against peaceful worshippers."
"The US stands firmly with the Egyptian government and people to defeat terrorism," the Embassy said in a statement.
The explosion comes weeks before the visit of Pope Francis to Egypt on April 28-29.
Palm Sunday falls on Sunday before the Easter. The feast commemorates Jesus' triumphal entry into Jerusalem, an event mentioned in each of the four canonical Gospels.
Coptic Christians make up about 10 per cent of Egypt's population of 85 million.
Egypt's Christian minority has often been targeted by Islamist militants.
Egypt has seen a wave of attacks by militants since 2013 when the military toppled president Mohammed Morsi, an elected leader who hailed from the Muslim Brotherhood, and launched a crackdown against Islamists.
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