While one war has been going on in Lebanon, a much different but bitter conflict has been raging inside Israel, complete with charges of anti-Semitism, comparisons with the Nazi Holocaust and a near-physical confrontation.

A parliamentary committee brought the issue to a head today, voting 11 to 10 its final approval for a Cabinet resolution to prohibit flights by the national airline, El Al, on the Jewish Sabbath, from dusk Friday to dusk Saturday, and on holy days.

Dozens of El Al workers gathered outside the committee chamber and yelled such virulent abuse that Israeli radio censored it off the air. Police were called to the scene. El Al employes briefly shut down the airline's operations out of Ben-Gurion International Airport near Tel Aviv and vowed to continue to fight the government order.

The impetus for the shutdown comes from Orthodox elements seeking to effect the biblical injunction against work on the Sabbath. But for El Al, whose operating losses amounted to $47 million the past fiscal year, the price of Orthodox purity would be high.

Basing its findings on information supplied by the airline, an economic committee of the Knesset, the parliament, estimated that closing down its operations on Saturdays and Jewish holy days could cost El Al up to $40 million a year.

Tourism losses to Israel, already down because of the war in Lebanon, could amount to $150 million more a year, the committee estimated. A committee of El Al workers also has estimated that the reductions in flights could cost the jobs of 900 of El Al's 4,700 employes.

After simmering for months, the dispute erupted dramatically 12 days ago, when hundreds of El Al workers blocked ultra-Orthodox Jews, identifiable from their beards, black skullcaps and black coats, from the Ben-Gurion terminal to board flights.

Charging that they were the victims of "religious coercion," the airline employes taunted their targets with references to the fact that Orthodox students of religion are exempt from military service in Israel.

The two-hour confrontation provoked a storm of protests, particularly from the ultra-Orthodox Agudat Israel political party, the prime mover behind the ban.

Rabbi Menachem Porush, a member of the Knesset, said of the demonstration, "We thought that in this generation we'd never see people pointing at us and saying, " 'He's a Jew and therefore will not enter.' "

The dispute reflects not only a split between Israel's Orthodox and secular Jews but also some of the peculiarities of Israeli politics. El Al became a target for an Orthodox campaign virtually to eliminate Saturday travel because the 1981 elections handed the Agudat Israel party an opportunity to exercise disproportionate leverage in the government.

In forming his coalition, Begin had to turn not only to the National Religious Party -- traditionally a part of Israeli governments--but also to the more extreme Agudat Israel party, whose four votes in the Knesset were crucial.

In return, Agudat Israel received, among other things, a commitment that the government would shut down El Al on Saturdays and holy days. The ban is to take effect the first Friday of September, and all Sabbath and holy day flights are to end by Feb. 1.

The holy days are the Jewish New Year, Yom Kippur, Sukkot, Passover and Shavuot.

Norm Klieman, a spokesman for the government-owned airline, said El Al considered the shutdown move "unfair and inequitable," noting that Jewish employes of other airlines serving Ben-Gurion Airport would be allowed to continue to work.

He said the shutdown would hit El Al particularly hard because the bulk of its Saturday passengers are Christian pilgrims and vacationers from Europe who travel on that day after completing their workweek.

Beyond this, Klieman said, there is a growing concern that if El Al is shut down on Saturdays the Orthodox community will quickly turn to other targets in its drive to keep the Sabbath observance pure. "The average citizen is worried," he said.