It is a long way from a defiant cry of "blood libel" hurled at critics to the sobering provisions of section 15(a) of Israel's commissions of inquiry law, but that is the distance the government of Prime Minister Menachem Begin has been moved in the last two months by three persistent men.

The cry of "blood libel" was the Begin government's initial response to charges that Israel bore some responsibility for the mid-September massacre of hundreds of Palestinian refugees in West Beirut by its Lebanese Christian allies.

But in an investigation that began Oct. 7 and has involved 42 primary witnesses, dozens of others who were questioned by staff investigators and hundreds of hours of testimony, a three-member Israeli commission of inquiry found section 15(a) more relevant. Under it, the panel last month issued warnings to nine senior government and military officials, including Begin, Defense Minister Ariel Sharon and Foreign Minister Yitzhak Shamir, as it was required to "where it appears to a commission of inquiry that a particular person is liable to be harmed by the inquiry or by its results."

On Sunday, the inquiry board--composed of Israeli Supreme Court Chief Justice Yitzhak Kahan, Justice Aharon Barak and reserve Army general Yona Efrat--is to begin the climactic stage of gathering evidence in the investigation. It is scheduled to hear testimony from witnesses called by some of the nine officials to establish their defenses, ending with reappearances before the panel by six of the nine.

Where the investigation will lead eventually is a favorite guessing game in Israel, although no one pretends to know the answer. The commission is strictly an investigative unit with no power to level formal charges against any of the individuals.

But the political implications of its findings, for the individuals involved, the Israeli Army and the Begin government as a whole, are another matter. Here, too, predicting the outcome is largely guesswork, but it is widely assumed that the warnings to the top echelon of the government and the military were not issued lightly and that all nine are in danger of being criticized.

With the warnings, the burden of proof shifted dramatically to Begin and the others, all of whom have been told they may be found to have been negligent in connection with the slaughter.

In addition to Begin, Sharon and Shamir, the civilian troika that runs Israel's foreign and defense policy, others who received the warnings are: Lt. Gen. Rafael Eitan, the Army chief of staff: Maj. Gen. Amir Drori, the Army's northern commander: Maj. Gen. Yehoshua Saguy, the chief of military intelligence: Brig. Gen. Amos Yaron, commander of all Israeli forces in Beirut: the head of Israel's intelligence service, the Mossad, who by law cannot be named in public, and Avi Dudai, Sharon's personal assistant.

Eitan and Yaron were warned of a possible finding of the more serious charge of "breach of duty" as well as negligence.

Throughout the investigation, the inquiry board has concentrated on two key questions. The first is whether the Israeli government erred in the first place in allowing Christian Phalangist militia units into the Sabra and Shatila refugee camps, particularly in light of the history of hatred between the Lebanese Christians and the Palestinians and the assassination of the Phalangist leader, Lebanese President-elect Bashir Gemayel.

The second is whether key officials in the government and the military failed to act on reports of the killing that surfaced on Sept. 16, the first night of the massacre, and reached the cabinet level by noon Sept. 17, about 18 hours before the slaughter ended.

The full extent of the investigation is not known, but from the public record alone that has been compiled by the inquiry board, and the tone of the panel's questioning, the tentative answer to both questions appears to be yes.

Begin and his colleagues maintain they never dreamed the Phalangists would go on a rampage and had no reason to consider this possibility. But in offering this defense, they have been trapped in an inherent contradiction. For the reason the Israeli government gave for sending its Army into West Beirut on Sept. 15 was to prevent chaos and bloodshed in the immediate aftermath of the Gemayel assassination.

Surely, the inquiry board members have asked in a variety of ways, the Palestinian refugees should have been considered among the most vulnerable residents of West Beirut and Gemayel's armed followers, the Phalangist militiamen, among the most dangerous.

Begin acknowledged in testimony that he had assumed "acts of revenge" would follow Gemayel's death. Sharon conceded that he anticipated civilian casualties from the Phalangists' action in the camps, but not the 700 to 800 deaths he said Israeli intelligence estimates took place.

Begin, Sharon and Eitan, the commission said in its warnings, appear to have "ignored the danger of acts of revenge and bloodshed" when they made the initial decision to send the Phalangist militia units into the camps, ostensibly to root out the remaining Palestinian guerrillas. Judging by the content of the warnings, the commission members also believe that neither Saguy, the chief of military intelligence, nor the head of the Mossad sufficiently warned others in the government of the danger of massacre.

According to the board's public record, many warnings were available to Israeli officials by about noon Sept. 17. Yet early that afternoon Yaron allowed the Phalangists to rotate fresh troops into the camps and to restock their ammunition. And at 4:30 p.m. Sept. 17, Eitan "congratulated" Phalangist commanders on the operation and authorized them to stay in the camps until 5 a.m. Sept. 18.

Sharon testified he knew nothing of all this until 9 p.m. Sept. 17. But he was nonetheless warned by the commission of a possible finding of failure to "order that the Lebanese Forces be removed from the camps as quickly as possible . . .when he received reports of acts of killing or acts which deviate from regular combat operations."

This public record clearly contains a number of serious implications for the nine officials. In the next stage of the investigation, beginning Sunday, they have been invited by the board to reappear for additional testimony, present new evidence or cross-examine other witnesses.

In his reply Begin reiterated his assertion that there was no reason to anticipate a massacre and said the government had "authoritative information" that about 2,000 Palestinian guerrillas were concentrated in the area.The investigation has become a shadowy but real presence in Israeli public life and is affecting the actions and reactions of those most directly involved.

Tuesday, testifiying before a parliamentary committee, Sharon suggested the Reagan administration is waiting for the board's findings to weaken the government and make it more susceptible to pressure.

Along with the head of the Mossad and Dudai, the Army officers' careers seem most in jeopardy at this stage. But there is in Israel today a determination that the Army not be made the sole "scapegoat."

That determination stems from an investigation by an inquiry into military and intelligence failures in the 1973 war. Although the electorate eventually took revenge on the then ruling Labor Party, it was the Army that bore the brunt of the criticism in that investigation.

Much will depend not only on whether the inquiry board follows its warnings with corresponding conclusions, but also on the manner in which it characterizes the degree of any negligence of duty it finds. A severe and direct criticism could not be swept aside and could conceivably tear the government apart.