Netanyahu and Turkish Prime Minister Recep Tayyip Erdogan spent about half an hour on the telephone during U.S. President Barack Obama's visit to Israel, U.S. officials said. Obama joined the conversation at one point.
Erdogan accepted the apology, officials said, and Netanyahu's acknowledgement of "operational mistakes" during Israel's stopping of the flotilla in 2010.
Netanyahu made the call from a trailer at the airport shortly before Obama's departure, The Wall Street Journal reported.
"In light of the Israeli investigation into the incident, which pointed out several operational errors, Prime Minister Netanyahu apologized to the Turkish people for any errors that could have led to loss of life and agreed to complete the agreement on compensation," Netanyahu's office said in a statement said.
Turkey has long been one of Israel's few allies in the Middle East but the deaths in 2010 after Israeli forces boarded the boats strained the two countries' relationship.