Pope and Peres are now holding their private meeting before making public remarks at ceremony outside.
On Sunday, Francis invited Peres and Palestinian Authority President Mahmoud Abbas to visit the Vatican to pray for peace, and both accepted.
Officials say the meeting will take place on June 6.
A Vatican spokesperson told reporters the invite to Peres and not Netanyahu was not a slight, but a sign of the close friendship between the pontiff and the president.
“The pope has with President Peres a good feeling, this is clear,” the spokesperson said, according to The New York Times. “This is not an exclusion of the other, but there are good premises to pray together with President Peres and Mahmoud Abbas.”
— Shimon Peres (@PresidentPeres) May 26, 2014