Before 1946, the Department of Antiquities was jointly staffed by citizens of the United Kingdom, Arabs, and Jews. After the creation of the Hashemite Kingdom of Jordan and the state of Israel, the Department was split into several smaller departments. According to Hallote and Joffe, Israel's Department of Antiquities and Museums "attracted relatively little attention from religious Jews," and a 1950s excavation of burial caves at Beth She'arim "did not elicit a great response from religious groups."(86–87) Israel also organized its archaeological activities so as to position the country's high culture on a global stage.(87) Politicization of archaeology, which Hallote and Joffe attribute to "popular interest of religious nationalist groups," did not begin in earnest until after the Six-Day War.(89)
Yigael Yadin, a professor of archaeology at Hebrew University, had previously been chief of staff of the Israeli Army. As an archaeologist, in 1960, he discovered papyrus scrolls written by Shimon bar-Kochva, a commander in the Jewish Revolt. The find was kept secret for a month, before being revealed at a ceremony attended by various Israeli leaders and the international media. A subsequent Yadin lecture at the Mann Auditorium in Tel Aviv attracted around three-thousand people.
Beginning in October 1963, Yadin led excavations at Masada, which currently serves as the swearing-in site of new Israeli Defense Forces soldiers. Personnel and resources were provided by the Army during the digs; the first ended in May 1964, and the second lasted from November 1964 to April 1965. Upon publishing his findings, Yadin commented on the religious and political relevance of the site, calling it "an undying symbol of desperate courage, a symbol which has stirred hearts throughout the last nineteen centuries."
The excavations were noted worldwide, and Yadin parlayed his new fame into a political career, eventually becoming deputy Prime Minister to Menachem Begin. Nachman Ben-Yehuda later argued that Yadin discredited Josephus' assertion that the rebels in Masada were Sicarii. Yehuda charged that Yadin "certainly used his very high credibility" as a veteran and professor "to bulldoze his overhauled version of Josephus Flavius concerning the events at Masada." Abraham Rabinovich credits the later excavations for "opening the way for the desert mount's becoming a major tourist site."
In 1967, the Six-Day War caused significant disruptions in archaeological activities in the region. American students and personnel at Hebrew Union College were urged to evacuate, and a planned excavation of the Gezer site, on June 26, was cancelled. The British School of Archaeology in Jerusalem suffered only minor damage, but the Palestine Archaeological Museum fared worse. As William G. Dever reports, "the exterior of this beautiful building was pock-marked by small-arms fire, particularly around the inner courtyard, and...the tower, which had been used as a gun position by the Jordanians, was rather badly damaged....Precious objects...lay broken by ricocheting bullets....The Dead Sea Scrolls Gallery was empty." The breakout of the war prompted indefinite suspension of excavation in the West Bank.
Excavation activities resumed on June 15, at Givat Shaul, followed by the resumption of work at Gezer on July 17. July 20 saw the initiation of a project at Tel Arad. After Israeli forces had gained control of the West Bank, the Israel Department of Antiquities laid claim to the area's notable archaeological sites. According to Dever, Israeli archaeologists hadn't had access to the sites since 1948. Subsequently, groups of experts visited Gibeon, Samaria, Shechem, and Tell Fa'rah, and an "emergency survey" of archaeological sites (so-called because it was assumed that the captured territories would soon be returned to Jordan) was put into motion, eventually recording some 6,000 sites, of which 5,000 were previously unrecorded.
Religious opposition to certain archaeological practices in Israel began in the late 1970s and intensified through the 1980s. Objections were raised to the excavation of the City of David in Jerusalem, for which project director Yigal Shiloh was publicly vilified. The situation escalated in 1981 when members of several different religious sects threw stones at archaeologists at the site. The confrontation, led by Shlomo Goren and Ovadia Yosef, resulted from the sects' allegation that the excavation was affecting a Jewish cemetery (which Hallote and Joffe claim did not exist). Education Minister Zevulun Hammer eventually ordered the excavation to be halted, but the High Court of Israel overturned his decision. Throughout the 1980s, activists identifying with the ultra-Orthodox Haredi movement were supported by Toldot Aharon and Agudat Israel in clashes at archaeological sites. Notably, in 1983, activists in Jerusalem damaged archaeologists' offices and graves in which archaeologists were buried.
By 1987, protests had reached American excavations at Caesarea. Archaeological operations were curtailed by the start of the First Intifada later that year. In 1992 a Greek mosaic was damaged in retaliation for the discovery of a crypt containing human bones under an Armenian church.
"Operation Scroll" is the term for a 1993 effort by the Israeli Antiquities Authority to discover more of the Dead Sea Scrolls in the Judean Desert. Several archaeologists searched between Wadi ed-Daliya and Nahal Deregot, surveying six hundred and fifty caves and sites, and ultimately excavating seventy of them. The earliest finds were from the Neolithic era, and there were many artifacts unearthed from the time of Bar Kokhba. At approximately the same time as this operation, the Oslo Accords were being written; the IAA was subsequently criticized for taking advantage of the timing. In November 1993, ultra-Orthodox Jews rioted in Jerusalem in response to archaeologists' allegedly excavating Jewish graves. Demonstrations in the city were organized by the Atra Kadisha religious group. Operation Scroll came under fire for possibly defying a new agreement reached by Israel and the Palestinian Liberation Organization regarding Palestinian self-rule, and may have circumvented a United Nations resolution that prohibited unearthing and removal of significant artifacts from occupied areas under foreign control.
In an archaeological context, animosity has existed between Israeli journalists and officials and their Palestinian counterparts, particularly from the 1990s into the 2010s. In a 1992 article in Ha'aretz, Israeli journalist Yosi Torpstein examined what he called "the large-scale theft of antiquities" by Palestinian looters. American academic Nadia Abu El Haj describes "Operation Scroll," a 1993 "salvage excavation" in Jericho that was launched in advance of Israel's pullout from the West Bank town. Abu El Haj's 2001 book Facts on the Ground was released to some controversy; archaeologist Alexander H. Joffe published a highly-critical review in which he described Abu El Haj's methods as "schizophrenic" and asserted that the book is "a representation of Israeli archaeology that is simply bizarre." Facts on the Ground won the Albert Hourani Book Award for 2002.
Several sites of archaeological significance have been targeted in apparent price tag attacks in the region, which have allegedly been carried out by what Ha'aretz termed "Hard-line Jewish youths." In December 2011, arsonists attempted to set a Palestinian mosque on fire in the West Bank, near Ariel. Palestinian witnesses reported that Israeli settlers were responsible for the predawn attack, in which several of the mosque's windows were broken and its entrance sustained burns. One week later, the Nebi Akasha Mosque in central Jerusalem was burned. The mosque, located in an Ultra-Orthodox neighborhood, was built in the 12th century and expanded in the 13th century. It was reportedly built on a burial ground for soldiers allied with Saladin. In September 2012, graffiti was sprayed on a mosque in Dura, near Hebron. The vandalism referred to the then-recent evacuation of the Migron settlement in the West Bank. Vandals attempted to burn down the mosque and nearby vehicles.