Turkey cautioned on Monday against what it described as Greek provocations in a longstanding dispute in the Aegean Sea, after Ankara said it had removed a Greek flag that had been hoisted over an uninhabited islet.

Turkey and Greece are NATO allies but they have been at odds over a host of issues from ethnically split Cyprus to sovereignty over airspace. They came to the brink of war in 1996 in a dispute over islets in the Aegean, although tensions have since eased.

"There was an attempt to plant a Greek flag on an uninhabited islet. In response, our coast guard teams made the necessary intervention and took that flag from there," Prime Minister Binali Yildirim told reporters.

"Our recommendation to Greece is that, within good neighbourly relations, it refrains from provocations that will increase tensions; that they act in line with the law of neighbourliness."

Three youths had hoisted the flag on the highest point of the islet, known as the Mikros Anthropofas, on April 13, Samos 24, a Greek website, reported.

Although Yildirim said the flag had been removed, Greek media cited some people on nearby islands saying it was still there.

Athens said that Yildirim's comments themselves were provocations.

"According to the latest briefing by the defence ministry and the navy to the Greek Prime Minister, no incident of violation of Greek soil has been confirmed. However, we continue to look into the matter calmly and seriously," the Greek government spokesman told reporters.

"In any case, I have to say that Mr. Yildirim's statement is absolutely provocative and condemnable," he said, adding Greece would not accept any kind of challenge to its land sovereignty.