The bombing appeared to be the second attack targeting Egypt’s Coptic Christians, after a bomb in a church in the Nile Delta town of Tanta killed 26 people and wounded more than 70.
The ministry said the explosion went off at Saint Mark’s Church in Alexandria, where Pope Tawadros II had earlier celebrated Palm Sunday.
No one immediately claimed either attack, but Islamic extremists have repeatedly targeted Egypt’s Christian minority in the past.
Islamic State affiliate based in the Sinai Peninsula claimed an attack on a Cairo church in December that killed around 30 people, and vowed more attacks on Christians.
Palm Sunday is one of the holiest days of the Christian calendar, marking the triumphant entrance of Jesus to Jerusalem.
The state-run Nile television channel said the blast struck the Mar Girgis Coptic Church in Tanta just before 10am (6.30pm AEST).
Provincial governor Ahmad Deif told the channel that the explosion occurred inside the church.
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