Merkel is scheduled to meet Egyptian President Abdel Fattah al-Sisi and then Coptic Orthodox Pope Tawadros II and Sheikh Ahmed al-Tayeb, Egypt's top Muslim cleric.
She will depart to Tunisia tomorrow to meet Tunisian President Beji Caid Essebsi.
Merkel is joined by a business delegation that could sweeten the diplomacy with investments badly needed by both countries, which are grappling with sluggish economies, jihadist attacks and high unemployment, especially among youths.
A major focus in Egypt and Tunisia will be on their troubled neighbour Libya, a largely lawless country that also has porous desert borders with Algeria, Niger, Chad and Sudan.
"Without a political stabilisation of Libya, we won't be able to stop the human traffickers operating out of Libya who are responsible for by far the most arrivals in Italy," Merkel said in her latest weekly podcast.
Since the 2011 overthrow of Moamer Kadhafi, Libya has been riven by power struggles, making it the main gateway for African migrants heading for Europe on dangerous Mediterranean crossings.
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