Jerusalem Affairs Minister Ze'ev Elkin has reportedly criticised organisers of the royal tour for, he claims, suggesting Jerusalem's Old City is in the Occupied Palestinian Territories.
In a statement to launch the trip Kensington Palace had said a day "in the Occupied Palestinian Territories will begin with a short briefing on the history and geography of Jerusalem's Old City from a viewing point at the Mount of Olives".
Many countries do not recognise Israel's annexation of East Jerusalem where the Old City and many holy sites sacred to a number of religions are found.
But the Israeli website Ynet news reported Mr Elkin as saying: "It is regrettable that in Britain they chose to politicise the royal visit.
"United Jerusalem has been the capital of Israel for 3,000 years and no distortion in the tour itinerary can change that reality."
Kensington Palace declined to comment.
William will begin his first full day in Israel on Tuesday visiting Yad Vashem, the World Holocaust Remembrance Centre, and will lay a wreath to commemorate the millions of Jews who died during the Second World War.
Later he will sit down for separate meetings with Israel's president and prime minister.
In the coming days he will also pay his respects at the tomb of Princess Alice of Greece, his great-grandmother and the Duke of Edinburgh's mother.
William will be following in the footsteps of Philip, who visited his mother's grave in 1994 when he travelled to Israel for a ceremony honouring her for saving Greek Jews during the Second World War.
The duke will be staying at Jerusalem's premier hotel the King David which has hosted everyone from US president Donald Trump to his Russian counterpart Vladimir Putin and the Prince of Wales.
Sheldon Ritz, the hotel's director of operations, writing in the Jewish News, said that William would be staying in a top-floor suite and that in total 50 rooms would be occupied by people associated with his trip.
The suites' windows have rocket proof glass and freshly made scones and the finest tea shipped from England will be available to make William's stay enjoyable.
Earlier in Jerash the duke strolled along the site's famous cardo maximus - the city's main thoroughfare lined with columns and still paved with the original stones complete in places with the grooves worn by chariots.
William was joined by Jordan's Crown Prince Hussein and when he reached the spot where a picture of Kate, Pippa and their father was taken he stopped and looked at a 2ft by 3ft enlargement of the image, released just before the Cambridges married in 2011.
The second-in-line to the throne laughed as he looked at the picture and then pointing at the image of Mr Middleton said to the Crown Prince: "Michael's looking very smart in his flip-flops."
In scorching sunshine and dressed in a smart casual look of jacket, shirt, trousers and sunglasses William recreated the photo by standing in the same spot as his wife when a child.
He smiled and said: "Need to come back with the family for this shot."
Kate's family moved to Jordan in May 1984 when she was aged two and her sister Pippa was just eight months old, after father Michael, a British Airways manager, relocated to the Jordanian capital of Amman for work.
The duchess went to an English-language nursery while her parents were in the country for almost three years, before they returned to Berkshire in 1986.
Samia Khouri, director of museums at Jordan's Department of Antiquities, guided the two princes around the sprawling site during a half-hour tour.
She said: "He was very surprised when he saw the photo, he did not expect that. But that's why he was here, because he wanted to take a photo at the same spot where Kate was photographed."