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Israel denied charges of a massacre, and a lone April 9 report in the Israeli press stating Foreign Minister Shimon Peres privately referred to the battle as a "massacre"[75] was immediately followed by a statement from Peres expressing concern that "Palestinian propaganda is liable to accuse Israel that a 'massacre' took place in Jenin rather than a pitched battle against heavily armed terrorists."[76]

Subsequent investigations and reports by the United Nations, Amnesty International, Human Rights Watch, Time Magazine, and the BBC all concluded there was no massacre of civilians, with estimated death tolls of 46–55 people among reports by the IDF, the Jenin office of the United Nations, and the Jenin Hospital.[77] A team of four Palestinian-appointed investigators reporting to Fatah numbered total casualties of 56,[65] as disclosed by Kadoura Mousa Kadoura, the director of Yasser Arafat's Fatah movement for the northern West Bank.

The UN report to the Secretary General noted "Palestinians had claimed that between 400 and 500 people had been killed, fighters and civilians together. They had also claimed a number of summary executions and the transfer of corpses to an unknown place outside the city of Jenin. The number of Palestinian fatalities, on the basis of bodies recovered to date, in Jenin and the refugee camp in this military operation can be estimated at around 55."[2] While noting the number of civilian deaths might rise as rubble was cleared, the report continued, "nevertheless, the most recent estimates by UNRWA and ICRC show that the number of missing people is constantly declining as the IDF releases Palestinians from detention."[2] Human Rights Watch completed its report on Jenin in early May, stating "there was no massacre," but accusing the IDF of war crimes,[78] and Amnesty International's report concluded "No matter whose figures one accepts, "there was no massacre."[3] Amnesty's report specifically observed that "after the IDF temporarily withdrew from Jenin refugee camp on April 17, UNRWA set up teams to use the census lists to account for all the Palestinians (some 14,000) believed to be resident of the camp on April 3, 2002. Within five weeks all but one of the residents was accounted for."[79] A BBC report later noted, "Palestinian authorities made unsubstantiated claims of a wide-scale massacre,"[13] and a reporter for the Observer opined that what happened in Jenin was not a massacre.[80]