Israel responded by saying the London-based rights group did not take into account the increasing number of attacks on its forces in the past year or seek comment until the eve of publication.
The report entitled "Trigger-happy: Israel's use of excessive force in the West Bank" documents the killing of 45 Palestinians and wounding of thousands "who did not appear to be posing a direct and immediate threat to life."
The report accuses Israel of "war crimes and other serious violations of international law" against Palestinians.
Since occupying the West Bank, east Jerusalem and Gaza in 1967, "Israeli authorities have signally failed to carry out independent investigations that meet international standards into alleged crimes," Amnesty said.
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The group calls on Israel "to open independent, impartial, transparent and prompt investigations into all reports of Palestinian civilians killed or seriously injured by the actions of Israeli forces."
It also urges the United States, European Union and the rest of the international community to "suspend all transfers of munitions, weapons and other equipment to Israel" to pressure it to change.
"During that year alone, 132 Israelis were injured, almost double the previous year," it added. "Over 5,000 incidents of rock hurling took place."
"In 2013 there were 66 further terror attacks which included shootings, the planting of IEDs (improvised explosive devices)... And the abduction and murder of a soldier."
Foreign ministry spokesman Yigal Palmor said Amnesty authored its report "without even bothering to ask for response and comment," until the eve of publication.