Sunday's 80-page report drew anger from the Arabs who make up a fifth of Israel's population and have long complained of discrimination by the Jewish majority.
The investigation looked into the killing by police of 13 Arabs in October 2000 during violent demonstrations in northern Israel in support of the Palestinian uprising that had begun a few days earlier.
"There is no alternative but to close all of the cases, some because of lack of sufficient evidence, and some because, to our regret, we have not managed to locate the responsible police officers," the report said.
Israeli Arab leaders condemned the report.
"For the future of our sons, we cannot keep silent in the wake of these findings," said Azmi Bishara, a member of Israel's parliament, urging protests and strikes to show the government it could not "forfeit the lives of Arabs".
Israeli police killed 13 Israeli
Arabs in October 2000
The October 2000 protests marked the biggest show of solidarity by Israeli Arabs for the Palestinian uprising against Israel. Protesters blocked highways and threw stones at police.
None of the demonstrators was found to have carried guns.
"We are not trying to justify shooting at demonstrators but we cannot rule out that in specific cases, such shootings are justified because there is a threat to life," said Justice Ministry official Herzl Shviro, who led the investigation.
Shviro said work was made more difficult because families had refused to allow autopsies.
In 2003, the government accepted a report that said the Israeli officers should be reprimanded for using excessive force but not charged over the killings.
"We are not trying to justify shooting at demonstrators but we cannot rule out that in specific cases, such shootings are justified because there is a threat to life"
Justice ministry official
Israeli Arabs became citizens of the Jewish state after its creation in 1948 in parts of the British mandate of Palestine.
Many of their kin fled or were driven to the West Bank, Gaza Strip and further afield in the Arab-Israeli war at the time.
There has been little direct involvement by Israeli Arabs in the Palestinian uprising, but some have been convicted for aiding bombers to carry out attacks in Israel.
Israeli Arabs have long complained of racism and institutionalised discrimination by Jews.
Relations took another blow last month when an ultranationalist Jew killed four Israeli Arabs on a bus in a vain attempt to wreck Israel's withdrawal from the Gaza Strip. A West Bank settler killed four Palestinians soon after.
The killings in the 2000 protests marked the deadliest action by Israeli forces against Israeli Arabs since 1956, when dozens were shot and killed after returning to Kafr Qasim village, then under martial law, after a curfew they said they were unaware of.
The officers involved in those deaths were sentenced at the time to several years in prison.