The Israeli government is preparing a formal complaint against the United Nations agency that aids Palestinian refugees in Lebanon, charging it allowed its schools and camps to be used as guerrilla arsenals and training grounds.

A high Israeli official said the protest against the U.N. Relief and Works Agency will be submitted during the next few days to the U.N. Secretariat in New York by the Israeli Foreign Ministry. It will allege that agency officials stood by while the Palestine Liberation Organization set up arms dumps and "terrorist schools" within U.N.-run camps and schools or vocational training centers, he added.

"They allowed their facilities to be turned into terrorist bases," the official said in a press briefing.

At the United Nations, the head of the UNRWA liaison office, John Miles, said his office was unaware of the Israeli complaint. He said UNRWA was conducting an investigation of some of the same charges made in press reports in Israel.

The charges are the latest in a series of confrontations between Israeli authorities and the U.N. agency. In the past, UNRWA has complained that Israeli officials obstructed its effort to aid Palestinian refugees, particularly in the Israeli-occupied Gaza and West Bank areas.

A year ago, for example, the agency's commissioner general, Olof Rydbeck, formally accused the Israeli military government in the West Bank and Gaza of victimizing innocent people by blowing up the homes of Palestinians accused of guerrilla activities. Israeli officials in response said that the agency, which employs many Palestinians and some Europeans sympathetic to the Palestinian cause, is biased against Israel.

UNRWA provides educational, health and relief services to nearly 240,000 registered Palestinian refugees in Lebanon. It helps administer 13 camps and 85 schools in Lebanon, with others in Jordan, Syria, the West Bank and Gaza.

Among the camps in Lebanon was Ein Hilweh near Sidon, which was razed by Israeli shelling and bombing.

The Israeli official charged that Ein Hilweh administrators knowingly allowed the PLO to store large amounts of arms and ammunition in underground caches there. Similar charges were made against the Rachaiyah camp near Tyre.

Israeli officials have been particularly incensed over what they call a "school of terrorism" in the Sibline vocational training center on a hilltop north of Sidon. Part of the facility was found to contain explosives, weapons and instruction manuals apparently for the use of PLO trainees, they said.

[Miles, in a telephone interview, quoted a statement by Rydbeck in the Jerusalem Post saying UNRWA is investigating press reports of the ammunition found in Sibline and seeking to determine if the reported arms were brought in before the school was forced to close in early June because of the fighting.]

["This agency is unaware of any unauthorized use of its vocational training center or any other of its installations in Lebanon," Rydbeck said. "Action would have been taken if such use had been detected. Arms were found in a dormitory in Sibline in 1975 and UNRWA closed all dormitories for 18 months."]