"It's quite normal for the two countries to talk for the normalisation of the ties. How can reconciliation be achieved without holding any meetings?" Turkish Foreign Minister Mevlut Cavusoglu told reporters in Ankara.
Cavusoglu's comments came a day after Israel's Haaretz daily reported that Israeli and Turkish officials had held secret talks in Rome on Monday in a bid to restore relations between the two countries.
Cavusoglu confirmed such a contact had been made and said: "These meetings are not new. Expert-level talks have been held between the two countries for a while."
In 2010, Israeli commandos stormed the Turkish-flagged Mavi Marmara, the largest ship in an aid flotilla for the besieged Gaza Strip.
Nine Turks died in the raid and one more died in hospital in 2014 after four years in a coma.
The assault sparked widespread condemnation and provoked a major diplomatic crisis between the two countries.
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Ankara expelled the Israeli ambassador, demanded a formal apology and compensation and an end to the blockade on the Gaza Strip, which is ruled by Hamas, a Palestinian militant group.
Talks on compensation began in 2013 after Israel extended a formal apology to Turkey in a breakthrough brokered by US President Barack Obama.
The Israeli government reportedly presented a deal to pay compensation to the families of the victims, but an agreement has not yet been forthcoming.
"The ball is in the court of the other side on our two demands (the lifting of the blockade on Gaza and the payment of compensation to the families)," Cavusoglu said.
"We are waiting for an answer from them. An agreement could perhaps have been reached much earlier but the process has been delayed because of the domestic balances of Israel," he said.
The talks come two weeks after the ruling Justice and Development Party (AKP), co-funded by Turkish President Recep Tayyip Erdogan who is known for his angry outbursts at the Jewish state, lost its majority in parliament.