Israeli Prime Minister Shimon Peres faced a growing revolt within his own Labor Party today over the presidential pardons given to the chief of Israel's secret security services and three of his deputies who had been accused of covering up the beating deaths of two handcuffed Arab prisoners in 1984.

Amid a mounting furor both from the opposition parties and within his own Labor Alignment, Peres and his Likud partners in the "national unity" coalition government continued to defend yesterday's decision by President Chaim Herzog to issue blanket, protective pardons to Avraham Shalom, chief of the Shin Bet security services, and three of his deputies. The pardons absolve them of any criminal liability in the alleged cover-up of the April 12, 1984, killings of two Palestinians taken prisoner after a bus hijacking.

Peres, speaking at a police awards ceremony here, said that in principle, he has never opposed an investigation of the responsibility of political officials, but that he was trying to protect the security services from disclosures that could compromise their effectiveness. Peres said that the political level of government had to support the security branches in disputes over operational matters, but that changes in the system were ultimately the responsibility of the legislature and the judiciary.

Foreign Minister Yitzhak Shamir, who was prime minister at the time of the incident and who is scheduled to replace Peres on Oct. 25, called Herzog's decision "a great and patriotic act."

Speaking before an assembly of the Jewish Agency here, Shamir said a thorough investigation of the alleged cover-up would touch on "the most vital problems of security in Israel" and would compromise the state's war against terrorism.

Shamir, who some Cabinet ministers have suggested participated in the alleged cover-up when he was prime minister, said, "I have no fears from any investigation. My position was and is that in the interests of the functioning of the security services . . . an investigation like this should be avoided to the extent possible."

However, a number of Labor Cabinet ministers, including Deputy Prime Minister Yitzhak Navon, demanded the empaneling of a special commission of inquiry to investigate the circumstances surrounding the killing of the two Palestinian hijackers after they were led off the bus and taken to a nearby field. Three of Shalom's former deputies have charged that the Shin Bet chief ordered that the prisoners be beaten to death, and then falsified evidence, suborned witnesses and perjured himself before two civilian inquiry committees and in an internal Shin Bet disciplinary court.

Joining Navon in demanding a full investigation were Energy Minister Moshe Shahal, Economics Minister Gad Yaacobi, Cabinet Minister Ezer Weizman -- all of the Labor Alignment -- and Communications Minister Amnon Rubenstein, of the Shinui Party, which is also a partner in the coalition government.

In addition, a number of Labor Party members of the Knesset (parliament) demanded a full investigation of the alleged cover-up. Some Labor Knesset members began circulating a petition to convene the party's ruling parliamentary caucus to discuss the controversy.

Shahal said he would propose the empaneling of a special inquiry commission at Sunday's Cabinet meeting to expose the circumstances of what he termed "a cover-up and a frame-up."

"I believe there was a very hard case of a miscarriage of justice," said Shahal, referring to charges brought against Maj. Gen. Yitzhak Mordechai, chief of the Israeli Army's paratroops and infantry. A military disciplinary board acquitted Mordechai last August of "violent behavior" and conduct unbecoming an officer after a civilian investigating commission accused him of beating the Arab prisoners to death with the butt of his revolver.

Mordechai, who the civilian panel said had not used "unreasonable force," was at the scene of the hijacked bus, but Shin Bet officials since have testified that five agents of the secret security services, at the direction of Shalom, beat the Arab prisoners to death.