The official report into the May 31 incident, in which nine Turkish peace activists were killed in international waters, was set to be released later in the day by a military commission led by Giora Eiland, a retired Israeli general.
A civilian panel is conducting a separate investigation into the interception that triggered an international outcry and severely strained Israel's relations with its once-close Muslim ally Turkey.
Quoting from what it said were portions of the military commission's report, the Yedioth Ahronoth newspaper said the findings pointed to "flawed preparation (in intelligence) prior to the arrival" of the Turkish-flagged Mavi Marmara.
The "battle guidelines" issued to commandos who raided the vessel were flawed as was the intelligence.
Israel said the troops acted in self-defence in opening fire on passengers who attacked them with metal rods and knives as the Israelis boarded the ship.
Some of the commandos, the military said at the time, were armed with paintball guns -- but also carried pistols -- in anticipation of only light resistance.
Yedioth Ahronoth and other Israeli media reported that the Eiland commission's report would not call for any military personnel to resign. But the findings raised speculation that senior officers' careers could be affected.
In response to Western criticism, including from its biggest ally, the United States, Israel has since eased a land blockade of the enclave where 1.5 million Palestinians live, allowing most civilian goods through, while continuing to enforce the naval embargo.
Eiland's report is the first to be published in the affair.
The separate civilian Israeli panel is led by a former Israeli Supreme Court Justice Jacob Turkel and includes two international observers.
Turkey called the bloodshed Israeli "state terrorism", withdrew its ambassador and cancelled joint military exercises. Turkish officials have dismissed the Israeli probe, saying there would be little credibility in an inquiry conducted by Israel into the actions of its own troops.
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