Israeli Prime Minister Benjamin Netanyahu had disavowed remarks by Defence Minister Ehud Barak supporting the division of Jerusalem in a future peace deal with the Palestinians, officials said.

"The defence minister's comments were not coordinated with the prime minister," an official in Netanyahu's office told AFP, speaking on condition of anonymity.

On Friday, Barak told a conference in Washington that he supported a plan originally raised by US President Bill Clinton at the 2000 Camp David Summit, which would see Jerusalem as the capital of both Israel and a future Palestinian state.

"Jerusalem will be discussed at the end with... western Jerusalem and the Jewish (areas) for us, the refugee-populated Arab neighbourhoods for them and an agreed upon solution in the holy places," said Barak, a former Israeli premier from the dovish Labour Party.

But his comments to an audience that included Palestinian prime minister Salam Fayyad and US Secretary of State Hillary Clinton did not represent the Israeli government's position, the official said on Sunday.

"They represent the long-held views of the defence minister but don't represent the views of the government as a whole," he said.

Netanyahu holds that all of Jerusalem, including the eastern sector and the Old City with its holy sites, which Israel captured in the 1967 Six Day War, is Israel's "eternal and undivided capital."

This is the second time Netanyahu has had to distance himself from remarks made by a senior minister in recent months.

In September, he issued a statement saying that Israeli Foreign Minister Avigdor Lieberman's UN General Assembly speech, which outlined controversial proposals for an Israeli-Palestinian agreement including making mostly Arab regions of Israel part of a future Palestinian state, did not reflect the official Israeli position.