Controversy in Israel between secular and religious Jews, already simmering because of the government's planned shutdown of the national air line El Al on the Sabbath, flared again today as the Army prepared helicopter landing pads in a remote corner of the Judean desert for elaborate ceremonies to mark the burial next week of some 1,800-year-old bones believed to be those of Jewish fighters in the revolt against Rome.

Climaxing a long crusade by the Ashkenazi chief rabbi, Shlomo Goren, to properly inter the skeletons of warriors of Shimon Bar Kochba, who led the second Jewish revolt of 132-135 A.D., workmen began clearing landing sites for helicopters that will ferry 200 dignitaries to the inhospitable desert hills at Nahal Hever, near the Dead Sea, on Tuesday.

Secular members of Israel's parliament charged that $250,000 in public funds will be spent on the state funeral and burial of bones of disputed origin and some ecologists complained that lasting damage will be done to a nature preserve for what will amount to a one-hour ceremony.

The remains of about 40 skeletons were found in 1955 by archeologist Yohanan Aharoni in the Cave of Horrors on the southern face of Nahal Hever, and 19 more skeletons were discovered in the nearby Cave of Letters in 1960 by archeologist Yigael Yadin, who later served as deputy prime minister.

The bones, which were dispersed to Israeli medical schools for examination and then ignobly stored in cartons in the basement of the Department of Antiquities here, became the focus last year of an intensive campaign by some religious Jews to persuade the government to arrange a state funeral for the "Bar Kochba heroes."

In November, in what secular critics called a costly publicity stunt, the 65-year-old Goren was lowered into the almost inaccessible Cave of Letters by a winch and cable from an Israeli military helicopter. There he found some more bones--along with hundreds of pigeons--but he decreed that according to the Halakha (Jewish law), they should remain where the warriors fell.

Several prominent archeologists, including Yadin, scoffed at Goren's campaign and suggested that the bones may not have been of the Bar Kochba period after all. Yadin said he was not even certain that bones he found in excavations at the Masada fortress in the mid-1960s were those of the Jewish zealots who committed mass suicide there, and that one pile of bones he found on Masada's southern face was mixed with the bones of animals.

But Goren persisted in his campaign and the ministerial committee on symbols and ceremonies approved a state funeral for the Bar Kochba bones. Goren decreed that the site should be Nahal Hever, which has no access by road, and the preparations for the helicopter landings began. The previously excavated bones are to be buried beside the remains of the Roman camp on top of Mount Hever, just above the Cave of Letters.

About 200 guests, including Prime Minister Menachem Begin, leading members of parliament and senior Army officers will be flown to the site for the funeral. The skeletons will be borne in four caskets, each carried by six Army captains.

One of the parliamentary critics of the funeral, Mordechai Virshubsky of the centrist Shinui Party, demanded today that the ceremony be canceled, calling it an extravagant waste of public funds. Virshubsky complained that publicity surrounding Tuesday's event would hurt a current Army fund-raising drive to finance an education program for Israeli soldiers.

The Israel Society for the Preservation of Nature today condemned the funeral plans, saying that Army bulldozers would extensively damage an important nature reserve.

The society's secretary general, Yoav Saguy, first charged that 20 bulldozers were scraping helicopter landing sites, but an Army command spokesman said workmen were doing a minimal amount of earth moving.

"They wanted to make new roads and build new helicopter pads, which would do severe damage," Saguy said later in a telephone interview. "We complained, and they appear to have decided to do less work. We will see what happens."

Meanwhile, Hillel Nathan, a Tel Aviv University scientist, disclosed he still has the remains of 69 more skeletons found during the Aharoni excavations at the Cave of Horrors, and he suggested that if the government conducts a state funeral for the other skeletons, it should include at least some of his stored remains.

Meanwhile, controversy continued over the Cabinet's decision to halt, within three months, all Saturday flights by El Al, in accordance with a coalition agreement when the Agudat Yisrael Orthodox Party joined Begin's Likud government last July.

Transport Minister Haim Corfu said yesterday that El Al cannot survive losses resulting from a cessation of Sabbath flights and that the government will have to sell the national carrier if Begin goes ahead with his plan.

El Al is expected to lose $40 million this year, Corfu said, and would lose an additional $30 million to $40 million a year if it drops Saturday and Jewish holiday flights, which account for one-fourth of the airline's passengers.

Israel's labor federation, has asked the supreme court to block the move to cut Sabbath flights.