The Canadian Press obtained a draft itinerary for Baird's four-day trip to Israel, which starts Friday, and it lists an afternoon stop at the Dome of the Rock in Jerusalem. A separate stop Friday afternoon at the al-Aqsa Mosque is labelled "TBC" or to be confirmed.
The two destinations are part of a contested and historic hilltop that is considered holy by Jews and Muslims. Jews call it Temple Mount and to Muslims it is the Noble Sanctuary.
It has been the scene of violent clashes in recent months between Palestinian protesters and Israeli police. Tensions were elevated in October when the police killed a Palestinian man suspected of trying to kill a Jewish activist who was promoting more access to the site.
Two Israeli media reports this week quoted the country's police chief, Yohanan Danino, as saying in a speech that visits to the hilltop compound pose "an existential threat" to the Jewish state because of the ongoing tension.
Initially, Baird's spokesman would not say whether the minister was still planning to visit the sites on Friday, saying, "We don't comment on details of drafts of the minister's itinerary."
But in a follow up email Thursday evening, spokesman Adam Hodge confirmed Baird would not visit either place.
He offered no further explanation.
Prime Minister Stephen Harper also cancelled a trip to the Dome of the Rock during his visit to Israel a year ago because of security considerations.
The hilltop is revered in Judaism as the site of biblical Hebrew temples.
It is Islam's third-holiest site, after Mecca and Medina in Saudi Arabia, and is revered by Muslims as the place where the Prophet Muhammad ascended to heaven.
Baird's choice of destinations in Israel sparked controversy in April 2013 when he met an Israeli cabinet minister for coffee in East Jerusalem, territory that the Palestinians and the United Nations consider to be disputed land.
The Palestinian foreign ministry summoned the Canada's envoy to protest Baird's visit.
Baird's upcoming visit includes a stop in the West Bank capital of Ramallah on Sunday, where he is to meet his Palestinian Authority counterpart Riad al-Malki. In Jerusalem, he is also expected to meet other key Palestinian figures including former Palestinian Authority prime minister Salam Fayyad.
It will be Baird's first opportunity to meet Palestinian officials since the United Nations Security Council blocked a Palestinian effort to set a three-year deadline for the establishment of a Palestinian state on lands occupied by Israel.
Baird spoke out against the move, as he has with similar Palestinian statehood initiatives at the UN.
"Canada believes strongly in a two-state solution between Israel and the Palestinian Authority and that negotiations provide the only viable path to lasting peace," Baird said in a statement on Thursday.
"It is important that we create an environment that enables the private sector to develop key economic areas and create sustainable jobs that will form the foundation for economic growth."
Baird says he wants to strengthen Canada's partnership with Israel on a number of fronts, including security and trade.
When Baird kicks off his visit Friday, he will arrive in a country facing a national election on March 17.
Before departing on Tuesday, Baird is to meet the major candidates, including incumbent Prime Minister Benjamin Netanyahu as well as opposition leader Isaac Herzog and former foreign minister Tzipi Livni, who have formed an opposing coalition.
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