A statement from Netanyahu's office had said the premier would be "meeting Pope Francis next Wednesday at the Vatican" and with US Secretary of State John Kerry for updates on nuclear talks with Iran and negotiations with the Palestinians.
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But an official on Sunday told AFP no such meeting with Francis will be taking place, noting that audiences with the Pope must be arranged sufficiently in advance.
A spokesperson for Netanyahu refused to comment on the matter.
This was to be Netanyahu's first meeting with Pope Francis. On Thursday, Palestinian president Mahmoud Abbas met with the pope and invited him to the Holy Land. Israeli President Shimon Peres also invited Francis during a visit earlier this year, as did Deputy Foreign Minister Zeev Elkin.
Abbas is the fourth Middle East leader to have met Pope Francis after Peres, Lebanese President Michel Sleiman and King Abdullah of Jordan.
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