Israeli Prime Minister Menachem Begin warned today that if Christian Phalangists in Lebanon become endangered as a result of the withdrawal of Syrian troops from Beirut, Israel "will not be passive."

As if to underline the warning, the Israeli Air Force today sent a flight of jet fighters over Beirut in what military officials later described as a "routine reconnaissance patrol." Reports from Beirut said the Palestine Liberation Organization opened fire on the Israeli aircraft, but that no planes were hit.

Begin's warning was reminiscent of threats Israel made when it sent warplanes over Beirut's Moslem Quarter in July 1978 to signal its readiness to defend the Phalangists.

In his waraning today, made before the overflight, the prime minister said, "We shall not allow the Christian minority to be subjected to pogroms. We cannot tolerate the wiping out of the Christian minority."

Syrian forces have been the main component of an Arab League peace-keeping force since the 1975-76 civil war between rightist Christians and predominantly leftist Moslems.

Responding to questions posed at a luncheon with foreign correspondents, Begin also hinted that he will support a motion in the Cabinet Sunday that would permit Jewish settlers to live in Arab cities on the West Bank. This would reverse a policy that has prevailed under two governments since Israel occupied the territory in the 1967 Six-Day War.

Asked whether his implicit warning of Israeli intervention applied only to southern Lebanon -- which is controlled by the Israeli-supported Christian militias of Maj. Saad Haddad -- Begin replied, "Clearly it applies to the Christian in the south and the north of Lebanon."

"We don't know what is happening in Lebanon. We will try to find out their [the Syrians'] intentions. But if the Christian minority in either the south or the north is attacked, Israel will not be passive."

Observers here have noted that if the Palestine Liberation Organization decides not to challenge the fragmented regular Lebanese Army and the Christian militias in the north once the Syrians pull out, and instead moves its units south, Israel could feel its security endangered to the point where it would send troops across the border, as it did in March 1978.

For several days, Israeli political leaders and military officials have been issuing muted warnings that moving Syrian troops from Beirut and other coastal Mediterranean positions will leave a security vacuum that could lead to a resumption of the civil war.

Begin said the Israeli Army would be "on guard" as a result of the Syrian movement southeastward, but he branded as "completely baseless assumption" reports from Damascus that the redeployment is necessary to repel a planned Israeli attack on Syria.

"It never occurred to us to think of attacking Syria," Begin said.

Begin also said he has drafted a note of protest to Egypt over anti-Semitic statements in a Kuwati newspaper attributed to Egyptian Deputy Prime Minister Hassan Tohami. It is the first protest note between Egypt and Israel since the two former enemies formally began normal relations just 12 days ago.

Tohami, a Moslem fundamentalist who once proposed a march on Jerusalem of a million Moslems to compel Israel to withdraw from the Arab part of the city, was quoted by Al Siyassa as predicting the imminent collapse of "the demistate Israel" and calling Jews "treacherous and hypocritical."

While some Israeli sources have sought to minimize the importance of the remarks, citing Tohami's well-known eccentricities and his fondness for Eastern mysticism -- including his self-claimed ability to stop his own heartbeat at will and start it again -- the published remarks have generated a bitter reaction among some legislators who demanded an official protest.

Begin called Tohami's remarks "incomprehensible" and said they were in "flagrant contradiction to the spirit in which Israel and Egypt have worked together . . . to live in peace, friendship and cooperation forever."

On the issue of Jewish settlers in Arab cities, Begin refused to be drawn into a direct endorsement of a government policy shift. Nevertheless, the prime minister said the murder in Hebron last week of a 23-year-old yeshiva student compels the government "to undertake measures that much abominable acts will not be carried out again."

Begin said he agreed with a pledge by Defense Minister Ezer Weizman in parliament yesterday that "we have returned to Hebron and we shall stay there." The Cabinet is expected to consider moving Jewish settlers into five houses in exclusively Arab Hebron that were owned by Jews 50 years ago. Jews fled Hebron during the 1929 Arab riots, in which 67 Jews were massacred.

Weizman yesterday defended the Israelis' right to live in the West Bank cities of Hebron, Nablus and Ramallah, which until now have not been open to Jewish settlement.

News services reported the following Middle East developments:

Israeli authorities yesterday lifted for eight hours the curfew imposed on the West Bank town of Hebron after an Israeli resident of a nearby Jewish settlement was killed Jan. 31. The curfew had been lifted for 90 minutes daily to allow residents to buy food and other necessities.

Morocco's King Hassan II and many top aides left for Saudi Arabia for talks with King Khalid on the Afghan crisis and bilateral cooperation, sources in Rabat said.

Libya accused France of "invading" Tunisia and called for an urgent meeting of the Arab League council. France sent aid to the Tunisian government of President Habib Bourguiba after a Jan. 27 commando attack on the phosphate mining town of Gafsa. Tunisia blamed Libya for that attack.