The ministry said the blast, which occurred late on Saturday in the Egyptian capital, also wounded the commander of the bomb squad.
It came just two days before the Orthodox Coptic Church, the dominant denomination among Egypt's estimated 10 million Christians, celebrates Christmas.
The incident is likely to force authorities to further tighten security around churches.
No one immediately claimed responsibility for the blast, which bore the hallmarks of the Islamic State group.
IS has targeted Christians in Egypt over the past years, killing more than a hundred of them in attacks on churches and buses carrying pilgrims to remote desert monasteries.
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