UN member states adopted a resolution allowing the Vatican and the Palestinians, which both have non-member observer status at the United Nations, to fly their flags.
The resolution was championed by the Palestinians, who see the symbolic gesture as an important reminder at the world body of its campaign for statehood.
But the Vatican had distanced itself from the Palestinian drive at the United Nations, arguing that there was no reason to break with the 70-year practise of raising only the flags of member states.
"The Holy See and the United Nations secretariat have agreed that the flag will be raised with no ceremony" on Friday, said Archbishop Bernardito Auza, the Vatican's UN ambassador.
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"UN personnel will raise it at the same time they will raise the other flags that day," he told reporters today.
For their part, the Palestinians have invited hundreds of leaders to attend a formal flag-raising ceremony on September 30 in the presence of Palestinian president Mahmud Abbas.
The Vatican's ambassador made clear that it was at the United Nations' behest that the flag was being raised.
UN officials "think that the visit of the pope would be a momentous time to have the Holy See flag already raised even though we didn't plan to have it," said Auza.
"They suggested that they could do it themselves without a public ceremony, and of course we accepted that."
Auza said he is planning to attend the Palestinian flag-raising ceremony as the representative of the Vatican, which officially recognized Palestine as a state in 2013.
A total of 45 countries abstained including Germany, Norway and other European nations.