The money has been transferred to the account of the Turkish justice ministry, a foreign ministry official told AFP, asking not to be named.
Turkey and Israel signed a deal three months ago to restore ties which hit an all-time low after the 2010 raid by Israeli commandos on a Gaza-bound aid ship that left 10 Turks dead.
The Turkish government is due to pass on the compensation money to the families of the victims in due course.
While the blockade remains in place, Ankara has been able to resume delivery of humanitarian aid to the Palestinians through Israeli ports under the deal.
A final key element is the exchange of ambassadors, who were pulled out of Ankara and Tel Aviv in the wake of the crisis even though diplomatic ties were never fully severed.
The official said that a Turkish ambassador to Israel will be appointed "soon".
The normalisation agreement had been urged by the United States, which is keen to see its NATO ally, overwhelmingly Muslim Turkey, resume its previously tight relationship with Israel.
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