"The toll now is 29 dead and five injured," said health ministry spokesman Khaled Megahed.
Another health ministry official, Adel Khalifa, confirmed the toll and said the dead included Egyptians and Sudanese and "other African nationalities."
The incident comes months after the head of the EU's border agency warned that growing numbers of Europe-bound migrants were turning to Egypt as a departure point for the perilous journey.
At least 10 dead on migrant boat sinking off Italy
Smugglers often overload the boats, some of them scarcely seaworthy, with passengers who have paid for the journey.
More than 10,000 people have died crossing the Mediterranean to Europe since 2014, according to the UN.
With the closure of the Balkans route popular with migrants seeking to reach northern European countries, as well as an EU deal with Turkey to halt departures, asylum seekers have been turning to other options.
Eight dead, more than 20 missing after boat capsizes off Malaysia
"Egypt is starting to become a departure country," Frontex chief Fabrice Leggeri said in an interview with the Funke group of German regional newspapers in June.
"The number of boat crossings from Egypt to Italy has reached 1,000 (so far) this year," he said.
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