Avraham Shalom in a scene from the Oscar-nominated documentary "The Gatekeepers," about former heads of the Israeli security agency, Shin Bet. Mr. Shalom died June 19 at 86. (AP)

Avraham Shalom, who resigned in disgrace in 1986 as head of Israel’s domestic intelligence service after ordering the slaying of two Palestinian bus hijackers — and then trying to cover up the execution, died June 19 in Tel Aviv. He was 86.

The clandestine agency, Shin Bet, announced the death without giving the cause.

Mr. Shalom, who grew up in pre-independence Israel, spent his career working in the security establishment. He participated in the successful 1960 effort to swipe Nazi war criminal Adolf Eichmann off a street in Buenos Aires and fly him to Israel, where he was tried and hanged.

Much of Mr. Shalom’s work placed him at the forefront of a perpetual and shadowy battle that sought to keep a young nation alive amid neighboring Arab countries that didn’t disguise their hope for its destruction.

The Israeli occupation of the West Bank and Gaza starting in the late 1960s had an important role in shifting Shin Bet from a domestic intelligence-gathering operation into an organization working actively on hostile ground. The mind-set, experts said, was about foiling terrorist threats, acting preemptively if necessary, and using unconventional tactics to fulfill its mandate.

Tough-minded and a wily political infighter, Mr. Shalom took over Shin Bet in 1980 — an era in which Israel began fighting a war with Lebanon while combating Palestinian militants as well as right-wing Jewish extremists further stoking the embers of hatred.

The incident that defined his legacy was the April 12, 1984, hostage crisis that became known as the “Bus 300 affair.”

That night, four Arab gunmen boarded the bus en route from Tel Aviv to the Mediterranean port city of Ashkelon with more than 40 passengers and rerouted the bus to the Egyptian border.

State security stopped the bus near a Palestinian refu­gee camp about 10 miles north of the Egyptian border, and several passengers escaped. In the overnight confrontation that followed, the press and ranking government officials, including Mr. Shalom, came to the scene.

The militants threatened to blow up the bus if Israel did not release 500 Arab prisoners. Negotiations ensued until the next morning, when Israeli special forces stormed the bus and shot two of the suspects. A news photographer on the scene took a picture of the other two suspects being taken away, still alive. All the remaining passengers survived, except for a 19-year-old woman killed in the crossfire.

The two captive hijackers were handed over to Shin Bet and, while in Mr. Shalom’s custody, they were clubbed to death in a field. Shin Bet reportedly collaborated with the Israeli military to cover up the killings, insisting the militants had met their fate on the bus.

Defying censorship restrictions, Israeli newspapers began printing pictures that clearly disputed that version. An international uproar ensued, raising questions about whether Shin Bet viewed itself above the law and about the morality of actions taken in the interest of Israeli self-defense.

Mr. Shalom led an effort to blame an Israeli general who had beaten the men while trying to extract information about bombs on the bus. After a subsequent government investigation, members of the security forces were either exonerated at trial or found themselves politically inoculated at the highest levels of government.

Shin Bet answers directly to the prime minister, and Mr. Shalom said that he was acting on orders from then-Prime Minister Yitzhak Shamir, who denied blame.

Meanwhile, Shin Bet agents who went public with information that appeared to pin the killings on Mr. Shalom saw their careers ruined.

With a new attorney general threatening a criminal inquiry, Mr. Shalom offered his resignation in June 1986 to President Chaim Herzog in exchange for immunity from prosecution.

According to the Associated Press, Mr. Shalom wrote a letter to Herzog saying that “all my actions in the matter of bus 300 were carried out by authority and with permission.” He won a presidential pardon for himself and a few key subordinates — a decision derided by lawyers who questioned the authority to pardon those who have not been convicted of or charged with a crime.

The supreme court upheld the pardons, which were also supported by many Israeli political leaders on the grounds of intelligence community morale and state security.

Mr. Shalom was born June 7, 1928, in Vienna and moved with his family in 1939 to what was then the British mandate of Palestine. He served in the Palmach, the underground paramilitary force of pre-independence Israel, before joining Shin Bet in 1950.

He was on a temporary assignment with the Mossad — the Israeli intelligence agency — when he was recruited to the team that tracked down Eichmann, one of the key architects of the Nazi Holocaust.

Mr. Shalom’s wife predeceased him, and survivors include two children, according to the Associated Press.

During the past decade, Mr. Shalom became an outspoken advocate for peace with the Palestinians through a two-state solution, especially after the violent Palestinian uprising in 2000 known as the second intifada. He was critical of Prime Minister Ariel Sharon’s efforts to sideline Palestinian leader Yasser Arafat.

“We must once and for all admit that there is another side, that it has feelings and that it is suffering, and that we are behaving disgracefully,” Mr. Shalom told The Washington Post in 2003. “We have turned into a people of petty fighters using the wrong tools.”

Mr. Shalom further pressed his case in “The Gatekeepers,” Israeli filmmaker Dror Moreh’s Oscar-nominated 2012 documentary that featured six former Shin Bet chiefs talking, often ruefully, about the reasons for and impact of their tactics.

As the director kept pushing Mr. Shalom back in time, to speak in detail of the Bus 300 incident, the former Shin Bet leader became steely.

He said the terrorists that night had come into his charge nearly dead, beaten at the hands of the army. He told his men: “Hit them again and finish it.”

Asked about the morality of the act, Mr. Shalom replied, “In the war on terrorism, forget about morality. Find morals in the terrorists first.”