Two helicopters, three ships and a coastguard vessel scrambled after the makeshift boat sank off the Greek island on Friday with hundreds of people on board.
The International Organization for Migration (IOM) said the vessel was "believed to have left Africa with at least 700 migrants on board".
The Greek coastguard said on Friday night it had rescued 340 people and recovered nine bodies.
The survivors arriving in Egypt today were 26 Egyptians, two Sudanese, two Eritreans and an Ethiopian, a police official said.
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Hundreds of thousands of refugees have reached Europe via that route since the start of last year. The flow has dramatically dropped since the arrival of the NATO force and a deal between Turkey and the European Union that entered force on March 20.
The EU-Turkey deal set the stage for a renewed effort by Ankara to stop clandestine migrants setting off from the Turkish coast, in exchange for political and financial support from the EU.
More than 2,500 migrants and refugees have drowned in the Mediterranean this year while trying to reach Europe, while upwards of 200,000 have arrived by sea, according to figures from the UN refugee agency UNHCR.