The amount was paid to the bank account of the Turkish justice ministry, reported CNN Turk.
Meanwhile, Ankara could announce the name of the ambassador to be appointed to Israel in "one week or 10 days", the broadcaster cited a senior Turkish official as saying on Friday.
Turkey and Israel will simultaneously announce the appointment of ambassadors, said the official, who wanted to remain anonymous.
The financial compensation was one of the conditions made by Turkey to normalise diplomatic relations severed by the two countries after the May 2010 Israeli commando raid on the"Gaza Freedom Flotilla," which was trying to break the Israeli blockade on Palestinians in the Gaza Strip.
Under the reconciliation deal with Ankara announced in June after six years of strained relations following the incident, Tel Aviv accepted to pay compensation to the families of the Mavi Marmara victims.
Israeli soldiers will be exempt from legal and criminal responsibility and individual Israeli nationals also would not be held criminally or financially liable for the incident under the terms of the deal.
The deal was approved by President Recep Tayyip Erdogan in August and recently voted into law by the Turkish parliament.
