The UN cultural body UNESCO overrode Israeli objections on Friday to urgently grant world heritage status to a church in the Palestinian city of Bethlehem venerated as the birthplace of Jesus.

UNESCO's 13-6 secret vote to add the Church of the Nativity and its pilgrimage route to the prestigious list was received with a round of rousing applause and a celebratory fist pump by the beaming head of the Palestinian delegation, and deep disappointment from Israeli ally Washington.

"These sites are threatened with total destruction through the Israeli occupation, through the building of the separation wall, because of all the Israeli sanctions and the measures that have been taken to stifle the Palestinian identity," the Palestinian delegate said after the vote.

He called the vote a powerful sign that the international community had rallied to the Palestinian cause and was ready to accept it as an independent state with borders that included territories captured by Israel in the 1967 Six Day War.

"It is testimony to the fact that the world as a whole is intent on protecting Palestine... and making sure that the Palestinian state is created within the 1967 border the capital of which would be east Jerusalem.

The US delegation to UNESCO said it was ‘profoundly disappointed’ while stressing that ‘this body should not be politicised’.

The Israeli delegate for his part said the Jewish state supported awarding world heritage status to the ancient church under a completely different procedure that carried no implications for the Middle East peace process.

"The decision taken now was totally political and does great damage in our opinion to the (UN) convention and its image," the delegate said.

The bid – the first since the Palestinians won controversial membership of UNESCO in October 2011 – was submitted ‘on an emergency basis’ because the Palestinians say urgent restoration work is needed.

Their membership has cost the body tens of millions of dollars in lost funding from the United States.

Israel said the ‘emergency basis’ status essentially meant that the United Nations as a world body was backing the Palestinian view that the church was threatened by the Jewish state's troops.

It had proposed co-sponsoring the church's application at a future date – an idea whose prospects seem remote amid continuing stalemate in the gruelling Middle East peace process.

The three Churches involved – the Catholic as well as Greek Orthodox and Armenian – for their part have only given lukewarm approval to the idea because of the dangers the move potentially poses to their own rights to the shrine.

"It is impossible to inherently pass the sovereignty over the church by fiat from the Churches to a non-existent state," the Israeli delegate said after the vote.

"It is moreover irresponsible for the committee to cancel in a sleight of hand the status quo that organised the management of the Church of the Nativity for 500 years."

The Palestinian bid had faced other hurdles that included a negative report from the body that evaluates sites for UNESCO and reported disagreement among Palestinian leaders themselves.

The historic vote was preceded by an extended afternoon debate and then more than an hour of heated discussion over procedures.

The motion had required a two-thirds majority because it was overriding a draft recommendation by UNESCO not to support the Bethlehem candidacy because of the evaluation committee's report.

The Palestinian delegation promised more battles at UNESCO in the years to come.

"Palestine is rich in world heritage and we are therefore going to have other nominations," the delegate chief said.