Speaking to Al Jazeera, Mr Erdogan also said Turkey had taken steps to prevent Israel unilaterally exploiting natural resources in the eastern Mediterranean.
He spoke amid a growing row over Israel's refusal to apologise for a deadly raid on an aid ship last year.
Turkey has already cut military ties and expelled Israel's ambassador.
It has also said it will challenge Israel's blockade of Gaza at the International Court of Justice (ICJ).
Relations between Turkey and Israel have worsened since Israeli forces boarded the Mavi Marmara aid ship in May last year as it was heading for Gaza. Nine Turkish activists were killed during the raid.
Israel has refused to apologise and said its troops acted in self-defence.
In his comments to Al-Jazeera, Mr Erdogan said Turkish warships were "authorised to protect our ships that carry humanitarian aid to Gaza".