Local media said 78 Turkish nationals were among those participating in the flotilla.
Turkey said it was sending charter flights to Israel to repatriate hundreds of Gaza flotilla activists, after Israeli forces detained them in scenes that sparked international condemnation.
"We plan to bring our citizens and participants from third countries to Turkey via special charter flights we will organise today," Turkish Foreign Minister Hakan Fidan said in a statement.
Foreign ministry sources said "three flights" with a capacity for "more than 400 passengers" were being sent to Ramon airport some 20 kilometres (14 miles) from the southern Israeli resort city of Eilat.
Around 50 vessels set sail from Turkey on May 14 seeking to break Israel's blockade of the besieged Palestinian territory and were joined at sea by a handful of others.
