Israel's military failed to prepare adequately for what turned into a deadly raid on a Gaza aid flotilla, according to findings of a military inquiry quoted by the Israeli media on Monday.

The official report into the May 31 incident, in which nine pro-Palestiniam Turkish activists were killed, 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.

Israel has said its commandos were enforcing a naval blockade necessary to prevent weapons from reaching the Gaza Strip's Hamas Islamist rulers.

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 panel is led by a former Israeli Supreme Court Justice Jacob Turkel and includes two international observers.

Its narrow mandate does not include an examination of the political decision-making process behind the launching of the raid, although Turkel said it would call for Prime Minister Benjamin Netanyahu to testify.

Instead, it focuses on whether the naval blockade and the flotilla's interception conformed with international law. The panel also will investigate the actions taken by the convoy's organisers and participants.

Turkey called the bloodshed Israeli "state terrorism", withdrew its ambassador and cancelled joint military exercises.