GENEVA, Dec 16 (Reuters) - U.N. human rights chief Navi Pillay accused Israel on Tuesday of "unprecedented and deeply regrettable" treatment of a U.N. investigator it deported after barring him from crossing Israel to get to Palestinian areas.

Richard Falk, U.N. special rapporteur on human rights in the occupied West Bank and Gaza Strip, was stopped at Ben Gurion Airport near Tel Aviv on Sunday and denied entry to Israel and held separately from two accompanying U.N. staff.

The U.S. professor, who is Jewish, had angered Israel by making remarks comparing its forces' actions in the Gaza Strip to those of the Nazis in wartime Europe.

"His U.N. mobile phone was confiscated, making further contact between the U.N. and Professor Falk impossible until after his subsequent deportation to the United States on Monday," Pillay said in a statement issued in Geneva, adding she was taking the matter up directly with Israeli authorities.

Falk -- who as a U.S. citizen does not require a visa to enter Israel -- was kept in a detention facility at the airport, it said.

Falk, whose mission was at the request of the Palestinian Authority, reports to the U.N. Human Rights Council.

Israeli foreign ministry spokesman Yigal Palmor has said Falk was denied entry because his mandate was "profoundly distorted and conceived as an anti-Israel initiative".

"Special rapporteurs do not require a formal invitation by the Israeli authorities in order to carry out official missions to the occupied Palestinian territories," said Pillay, U.N. high commissioner for human rights.

His predecessors had been allowed to cross Israel on their way to the territories, she said.

The U.N. human rights office informed Israel in October and early December of Falk's intention to make his first official visit to the territories, but received no sign they would not allow him to transit until an email shortly before midnight on Saturday -- too late to be read before his departure, she said.

"It is the responsibility of states to cooperate with the independent U.N. experts appointed by the U.N. Human Rights Council. That is an important principle," Pillay said. (Reporting by Stephanie Nebehay; editing by Jonathan Lynn and Andrew Roche)

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