The committee found mistakes were made "at quite a senior level" but did not recommend punishments for any of the officers involved in the raid.
It also concluded that "the use of live fire was justified" and called the raid "estimable".
Lieutenant-General Gabi Ashkenazi, the Israeli army chief of staff, said in a statement that he accepted the report's conclusions.
IHH, the Turkish group which organised the flotilla, criticised the report's conclusions, particularly the claim that the Israeli army was justified in using live ammunition. Huseyin Oruc, a member of IHH's board, told Al Jazeera that the Israeli soldiers were responsible for starting the violence on board the ship.
"If you compare the passengers on the Mavi Marmara and the soldiers, even their equipment... you can understand how much balance there was between the two sides," he said.
Al Jazeera's Anita McNaught reports on Turkish activists' dismissal of the Israeli probe
Eight Turkish citizens and a joint US-Turkish national were killed after Israeli commandos dropped onto the vessel as it tried to enforce its naval blockade of the Palestinian territory.
Israel has previously claimed that the pro-Palestinian activists were shot dead after they attacked the troops with makeshift weapons, but those on board have said that the commandos attacked first.
The army investigation, led by Major-General Giora Eiland, is separate from the public inquiry being carried out by the government-appointed Tirkel Committee, which will decide whether the raid complied with international law.
Another probe, by the state comptroller's office, is expected to begin shortly.
Eiland presented the findings to the members of Israel's general staff, including Major-General Tal Russo, the head of Israeli military operations, and Major-General Amos Yadlin, a military intelligence official.
Israel has faced widespread international criticism over the deaths of the activists.
Turkey withdrew its envoy to Israel, later saying that the incident would leave an "irreparable and deep scar".
Amid an international outcry over the raid, Israel rejected a proposal by Ban Ki-moon, the UN chief, for an international inquiry, but appointed two foreign observers - David Trimble, a Northern Ireland politician and Nobel Peace Prize laureate, and Canadian jurist Ken Watkin - to the Tirkel Committee.
Mark Regev, a spokesman for the Israeli government, told Al Jazeera that Israel's internal investigations would be enough to properly evaluate the raid.
"Israel's investigatory process, both civilian and military, meets the highest international standards," Regev said. "It's standard operating procedure [to investigate] after any military operation, especially an operation that has human fatalities."
"We take this process very seriously."
Israel has said its commandos were enforcing a blockade necessary to prevent weapons from reaching Hamas fighters in the Gaza Strip, but has since eased its land border restrictions with the territory to allow through more civilian goods.