It added that the Israeli authorities had given no indication they would not allow Falk into the country, until an email was sent on Saturday at 11:03 pm (2203 GMT) to a staff member of the Office of the High Commissioner in Geneva, who was not in a position to read it before leaving with Falk early Sunday for Israel.
Pillay said she would raise the matter directly with the Israeli authorities, citing the "important principle" of cooperation with UN officials.
Falk, who is the UN's monitor of human rights in the Palestinian territories, last week prompted Israel's ire when he said its policies against people in the territories amount to a "crime against humanity."
The Israeli ministry said Falk's mandate is biased and that this is "further exacerbated by the highly politicised views of the rapporteur himself, in legitimising Hamas terrorism and drawing shameful comparisons to the Holocaust."
On December 10, Falk called on the United Nations to make an "urgent effort" to "implement the agreed norm of a responsibility to protect' a civilian population (in the Palestinian territories) being collectively punished by policies that amount to a crime against humanity."
Israel has sealed off the Gaza Strip from all but basic goods since the Islamist movement Hamas, which is pledged to its destruction, seized power in June 2007 after routing forces loyal to Western-backed president Mahmud Abbas.