Lipkin-Shahak was the great-grandson of Yitzhak Lipkin, an early pioneer to Palestine and businessman who financed the construction of the Ohel Shlomo and Shaarei Yerushalayim courtyard neighborhoods on Jaffa Road in Jerusalem at the end of the 19th century.

When it was discovered he had been serving as Director of Military Intelligence, and while battling it, then-Prime Minister Yitzhak Rabin allowed him to travel abroad for medical consultations.

[1] On 19 December 2012, Amnon Lipkin-Shahak died in Hadassah Ein Kerem Hospital in Jerusalem, after a long battle with cancer.

In April 1973, as a part of the Israeli raid in Lebanon, he assaulted PFLP headquarters in Beirut, and was decorated with a second Medal of Courage for "his leadership in action".

[6] During the Yom Kippur War, he served as deputy commander of the Paratroopers Brigade and fought in the Battle of the Chinese Farm, contained Egyptian forces at Ismailia, and defended the Sinai desert.

In 1991, he was appointed Deputy Chief of Staff, and during this role served as the commander of Operation Solomon, which brought 15,000 Ethiopian Jews to Israel.

[2] After retiring from the army he expressed dovish opinions and severely criticized Prime Minister Benjamin Netanyahu.

[1] In April 2008, Lipkin-Shahak signed a letter of support for the recently created J Street American Jewish pro-peace lobby group.