On 11 May 1960 Israeli agents kidnapped a middle-aged man called Ricardo Klement while he was walking home from a bus stop in a suburb of Buenos Aires; Klement was bundled into a car and taken to a safe house, where he admitted that his real name was Adolf Eichmann, the SS officer who played a leading role in implementing Hitler’s “final solution”.

In charge of the snatch squad was Rafi Eitan, who was to become a leading figure in Israel’s intelligence community. The capture of Eichmann and his subsequent trial in Jerusalem marked a great leap forward in popular understanding of the Holocaust.

Whether the trial revealed the “banality of evil,” in Hannah Arendt’s famous phrase, or simply added to knowledge of the Nazis’ industrial-scale extermination of Jews, it was a landmark event.

Eitan, who has died aged 92, revealed later that at the same time the Mossad secret service learned of the presence in Argentina of another notorious Nazi, Josef Mengele, who carried out gruesome medical experiments in Auschwitz. Eitan refused to kidnap Mengele as well for fear of jeopardising the Eichmann operation. He was standing behind the gallows when Eichmann was executed in 1962. Mengele died a natural death without ever facing justice.

Rafi Eitan, left, with Ariel Sharon in 1987. Photograph: Israel Sun/Rex/Shutterstock

The Eichmann kidnapping was Eitan’s best known secret mission, but neither his first nor his last. Many of them remain top-secret to this day. He was stocky, short-sighted and hard of hearing, but still served as an inspiration for thriller writers, such as John le Carré in The Little Drummer Girl.

Eitan was born in Kibbutz Ein Harod in British-ruled Palestine, to Yehudit Volwelsky and Noach Hantman, who had emigrated from Russia; Rafi later changed his surname to Eitan. In the 1940s he was recruited to the Palmach, the elite arm of the Jewish Haganah underground, where he acquired the lifelong Hebrew nickname of Rafi Hamasriah (“Rafi the Stinker”) from a fellow fighter.

Killing enemies was a habit he acquired early. When he was 19 he shot dead two Germans who belonged to the Protestant Templer sect to deter others from returning to Palestine after the second world war. “We did not feel any guilt,” he explained later. “On the contrary, we felt we were doing our duty as sons of the Jewish people.”

In the final years of the Mandate Eitan was involved in smuggling Jewish immigrants from Europe in defiance of the British blockade. In one of the operations a mine explosion badly damaged his ears.

In the war of 1948, which led to Israel’s independence and the Palestinian Nakba (catastrophe), he fought in several key battles. Like others of that generation he acquired a heroic aura that faded only decades later when revisionist Israeli historians gained access to the archives and took a warts-and-all look at that crucially formative period.

In 1954, working for the Shin Bet security service, Eitan took part in the abduction in Paris of an Israeli air force officer who was allegedly spying for Egypt. The officer was given an injection to sedate him on the military flight home, but it killed him and his body was dumped in the sea. The episode was covered up for decades. “Nothing done in the name of completing my mission bothered me,” he shrugged in a recent film interview.

From 1964 he served as head of Mossad operations in Europe, tracking and liquidating German scientists who were building rockets for Nasser’s Egypt. He requested, but was denied permission, to assassinate young Palestinian activists who had just formed the Fatah movement, the nucleus of the Palestine Liberation Organisation.

Adolf Eichmann was put on trial in Israel and executed in 1962. Photograph: Brook Lapping/Kessler Prod/BBC

In 1968 he was part of an Israeli team that visited the NUMEC nuclear processing plant in Pennsylvania shortly before the disappearance of 200 pounds of enriched uranium, enough to make six atomic bombs. He resigned from the Mossad when he was not promoted to head the service.

In 1976 when Ariel Sharon, a close friend, became adviser on security affairs to the Labour prime minister, Yitzhak Rabin, Eitan was his assistant. Two years later he became an adviser on terrorism to the Likud’s Menachem Begin. He was in that role when the Palestinian who was held responsible for the Munich Olympics massacre of 1972 – Ali Hassan Salameh – was tracked down and killed by a car bomb in Beirut.

Eitan’s career in the shadows ended badly. Running a body called the Bureau of Scientific Liaison, he was blamed for the scandal over Jonathan Pollard, a US naval intelligence analyst who was recruited on Eitan’s orders to spy on the US – a hugely damaging breach of the intimate relations between the two countries. Eitan, under the patronage of Sharon – then minister of industry – was appointed chair of Israel Chemical Industries.

In 2006, he followed other veterans of Israel’s security establishment and went into politics, founding the Dor party for pensioners. It won seven seats in the 120-member Knesset and benefited from the country’s system of proportional representation and coalition-building. He served as pensions minister, from the age of 80, until 2009.

Last year, he attracted angry criticism for endorsing the far right Alternative for Germany (AfD) party. The AfD, openly antisemitic and racist, was the first anti-immigrant, far-right party to enter the Bundestag since 1945.

On one view of Eitan, his not being a Holocaust survivor but a native born “Sabra” enabled him to take a pragmatic and unemotional view of working with Germans – in pursuit of what he saw as Israel’s best interests.

He is survived by his wife, Miriam Peled, and their three children.

• Rafi Eitan, intelligence chief and consultant, born 23 November 1926; died 23 March 2019