"Egypt is starting to become a departure country," said Frontex chief Fabrice Leggeri in an interview with the Funke group of German regional newspapers.
"The number of boat crossings from Egypt to Italy has reached 1,000 (so far) this year," he said.
"The route is gaining popularity. The crossing is extremely dangerous, the journey often takes more than 10 days," Leggeri said, adding that there were "few ships on this route that could save migrants from sinking boats".
Several North African ports, including Libyan ones, are gaining popularity as departure points, with Italy emerging as the key destination.
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"The central Mediterranean route has never been as popular," said Leggeri.
"Between 13 and 14 times more refugees are reaching Italy from Libya compared to migrants from Turkey to Greece," he said.
More than 10,000 people have died crossing the Mediterranean to Europe since 2014, the UN said in early June.