Turkey's Prime Minister Recep Tayyip Erdogan on Wednesday branded Israel as a "threat" to its region, accusing it of owning nuclear weapons, in a defence of Palestinians.

"I right now see Israel as a threat for its region, because it has the atomic bomb," Erdogan said in a foreign policy speech during an official visit to South Africa.

Israel has never officially admitting to possessing nuclear weapons, but is widely believed to be the only Middle East country to have them. Others including Iran, Iraq, Syria and Libya are suspected of trying, or having tried in the past, to follow suit.

Turkey downgraded relations with one-time ally Israel after the latter refused to apologise for its raid on a Gaza-bound Turkish aid flotilla, in which nine Turkish activists died on May 31, 2010.

Last month, Turkey expelled the Israeli ambassador and froze military ties and defence trade deals. Ankara has also threatened to send warships to escort any Turkish vessels trying to reach Hamas-ruled Gaza.

Erdogan's remarks came in response to comments from an Israeli embassy diplomat in South Africa, who blamed radical Islamic organisation Hamas for launching rocket attacks into Israeli territory.

"I have asked many Israeli officials, how many Israelis, have been killed by rockets launched from Gaza and Palestine. I could not get an answer," Erdogan said.

"Yet tens of thousands of Palestinians have been killed from bombs that have rained down on them from Israel."

"You sleep at night peacefully and secure," he told the diplomat, to applause by South African foreign affairs officials and members of the diplomatic corps.

"Yet Palestinians can't find a single trace of peace in Palestine."

Erdogan also accused Israel of committing "state terrorism", saying Israel had attacked the Hamas-ruled Gaza Strip as well as the UN buildings in Gaza with phosphorus bombs.

Erdogan in the past has accused the West of "double standards" in the way that it has tried to ban Iran from building nuclear weapons without taking similar measures against Israel.

He echoed those remarks on Tuesday at a press conference, where he said the United Nations had failed to implement its resolutions against Israel.

"Here I am talking about 89 resolutions of the UN Security Council and 247 resolutions of the General Assembly, none of which are implemented," he said.

"On the other hand you have resolutions for example about Iran, the Sudan and Palestine which are implemented."

But Erdogan said the Security Council should have approved a European-sponsored resolution condemning Syria's deadly crackdown on protests, which Russia and China blocked on Tuesday.

"The Syrian administration should have received a warning," he said.

"The people of that country do not need to endure a merciless, shameless, tyrannical regime that bombs its own country from the sea."

He declined to criticise his host South Africa for abstaining from the vote, but said: "My heart remains with those struggling for freedom. South Africans have been in that position."

"But this does not constitute an obstacle," he said, adding that "Turkey like some other European Union countries will take steps on this issue."

"We will inevitably impose right now a package of sanctions," he said.

In recent months, the United States has been alarmed at the estrangement between Turkey and its closest Middle East ally Israel.

Secretary of State Hillary Clinton is expected to urge Turkey to defuse tension and repair strategic ties with Israel when she visits Istanbul to attend a conference on Afghanistan next month.

Clinton will visit Turkey on November 2, Marc Grossman, US special representative for Afghanistan and Pakistan, was quoted as saying in the Turkish media.