For the second time in three days, Pope Benedict XVI stated his support for an independent Palestinian homeland during his Middle Eastern trip.

"Their legitimate aspirations for permanent homes, for an independent Palestinian state, remain unfilled," he said while at the Aida refugee camp, near Bethlehem on Wednesday.

On his trip to the town of Bethlehem, Benedict had to pass through towering walls of concrete, which are part of Israel's separation barrier to block off the West Bank's Palestinian areas.

Accompanied by Palestinian President Mahmoud Abbas, the Pope expressed regret over Israel's construction of the barrier.

"In a world where more and more borders are being opened up ... it is tragic to see walls still being erected," Benedict said. "How earnestly we pray for an end to the hostilities that have caused this wall to be built."

Israel says the barrier, which stretches hundreds of kilometres along the West Bank boundary, is needed to ensure security.

But the Palestinians say the wall is encroaching on their land, cutting off thousands from their farms and from public services and leaves about 10 per cent of the West Bank on Israel's side.

The Pope told Abbas the Vatican supported his people in their desire to live independently.

"Mr. President, the Holy See supports the right of your people to a sovereign Palestinian homeland in the land of your forefathers, secure and at peace with its neighbours, within internationally recognized borders," the Pope said.

He also made reference to the struggle Palestinians have faced in living under Israeli military rule.

"I know how much you have suffered and continue to suffer as a result of the turmoil that has afflicted this land for decades," the Pope said.

Wednesday's remarks followed a similar statement Pope Benedict made Monday morning when he arrived in Israel.

The Pope is in the middle of a week-long pilgrimage to the Middle East, his first official visit to the region since becoming pontiff.

It is Pope Benedict's intention to build interfaith relations during his trip.

But so far, the Pope's travels in the Middle East have seen several minor controversies, including criticisms of a speech the Pope gave at Israel's national Holocaust memorial, Yad Vashem, on Monday.

The German-born Pope was accused of not going far enough in speech to condemn Nazi atrocities that killed six million Jews during the Second World War.

On Tuesday, the Pope visited some of the holiest Muslim and Jewish sites in Jerusalem, the Dome of the Rock and the Western Wall.

With files from The Associated Press