Pope has 'no political agenda' in visiting Middle East: Vatican

Pope Francis "has no political agenda" in visiting the Middle East or making unplanned stops at Israeli or Palestinian landmarks, his office says.

Pope Francis prays at Israel's separation barrier on May 25, 2014 after he made an unscheduled stop at the security wall drawing attention to the towering eight-metre (26-foot) high concrete wall topped by a guard tower, in the West Bank town of Bethlehem. (AAP)

The Vatican is denying Pope Francis's Middle East trip has been driven by a political agenda, as Israel and Palestine indulge in point-scoring over his impromptu gestures.

Francis "has no political agenda" and his unscheduled visits to the West Bank barrier Israel is building and a memorial for Israeli civilians killed in militant attacks were "gestures" which "rounded out his official program," Vatican spokesman Federico Lombardi said on Monday.

On Sunday, Francis made an unplanned stop by the separation barrier, climbing out of his jeep to pray, his forehead and hand resting against the wall, in a powerful show of support for Palestinians.

His unscheduled stop on Monday at a national cemetery on Mount Herzl took place at the personal request of Israeli Prime Minister Benjamin Netanyahu to "balance" his trip, Lombardi said.

"I was not surprised to hear negative reactions in Israel over the pope's decision to stop and pray in front of the separation barrier," Lombardi said.

"The pope did not know about the (Israeli) memorial, and added it when it was possible."

The Pope is winding up a packed trip which saw him issue a unique invitation to the Israeli and Palestinian presidents to pray with him at the Vatican to end their "increasingly unacceptable" conflict.

Palestinian president Mahmud Abbas accepted, saying he will go to the Vatican on June 6.

Israeli President Shimon Peres also welcomed the invitation but his office has not specified a date.