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.
Eight Turkish citizens and a joint US-Turkish national were killed after Israeli soldiers dropped onto the vessel as it tried to enforce a 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 soldiers attacked first.
The raid, conducted in international waters, provoked a global backlash against Israel and prompted widespread calls for an
Al Jazeera's Anita McNaught reports on Turkish activists' dismissal of the Israeli probe
The Israeli government rejected the demands and instead ordered the military to launch an internal investigation, led by Major-General Giora Eiland.
It also set up a separate panel, the Tirkel Committee, which will decide whether the raid complied with international law.
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.
His report blamed bad intelligence for the fact that no "alternative operational courses of action other than a full boarding of the flotilla" was planned for.
"The operation relied excessively on a single course of action", the report said, but "emphasised the fact that as far as is currently known, no country in the world holds the ability to stop a vessel at sea in a non hostile manner".
It also praised the "the various stages of medical evacuation of the injured by air and by sea, including the injured passengers of the Mavi Marmara", but made no mention of those that died during the attack.
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 independent international inquiry.
However, two foreign observers - David Trimble, a Northern Ireland politician and Nobel Peace Prize laureate, and Canadian jurist Ken Watkin - were subsequently appointed 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 soldiers 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 previously banned goods.