Foreign Affairs Minister John Baird is shrugging off his less than cordial welcome in the West Bank.

Palestinian protesters hurled eggs and shoes at Baird's convoy in Ramallah, accusing Canada of siding with Israel.

The minister was not hit, and later joked that he got a lot worse when he was a cabinet minister in the Mike Harris government in Ontario.

Baird says his meeting today with the Palestinian Foreign Minister Riad Malki was "cordial and constructive" and said it included "candid and frank exchanges on areas where we differ in opinion."

The protesters held signs reading: "Baird you are not welcome in Palestine."

CBC's Derek Stoffel said Baird downplayed the incident while talking to reporters later in Jerusalem, after his meeting with Israeli Foreign Affairs Minister Avigdor Lieberman.

"Listen, I was in Mike Harris's cabinet for four years. I've had a lot worse," he said, referring to the man who was Ontario's premier from 1995 until 2002.

Activists from Palestinian President Mahmoud Abbas' Fatah party had earlier called for a boycott of the minister because of the Canadian government's perceived pro-Israel stance.

Baird is in the region for four days of meetings with Israeli and Palestinian officials.

A group of protesters gathered in Ramallah as Foreign Minister John Baird met with his Palestinian counterpart in the West Bank city. (Reuters)

Canada is opposed to the recent Palestinian bid to pursue war crime charges against Israel.

Baird's statement says he asked Malki to "strongly reconsider the consequences of moving forward with any action that may be counterproductive to a negotiated solution with the State of Israel."

It was also his first meeting with the Palestinian Authority since the United Nations Security Council blocked a Palestinian motion to set a three-year deadline for the establishment of a Palestinian state on lands occupied by Israel.

Baird has spoken out against the move, as he has with similar Palestinian statehood initiatives at the United Nations.

Canada was among a handful of countries that voted against Palestinians' successful bid to become a non-member state at the UN General Assembly in 2012. This month, Baird called a Palestinian move to join the International Criminal Court "concerning and dangerous".

He now heads back to Israel to continue his consultations.