The probe, meant to derive operational conclusions from the deadly events which took place aboard the Marmara – the sail's lead vessel – will be conducted by a panel of experts headed by Maj-Gen (ret.) Giora Eiland.
The move is somewhat exceptional, since the IDF is usually satisfied with internal inquests conducted by the units heading various operations.
Similar external inquires were conducted after Gilad Shalit's abduction and the Second Lebanon War.
Eiland and his team will review post-op debriefings and the initial investigation into the events, as well as the performance of all bodies connected to the operation.
The IDF said the decision to create the panel stemmed from the military's wish to investigate every aspect of the deadly raid in full.
Joining Eiland will be Brigadier-General Aviv Kohavi, who once headed the Operations Directorate, former Chief Intelligence Officer Brig.-Gen. (res.) Yuval Halamish and Colonel (res.) Ben Zion Da'abul, who held senior posts in the Navy and the defense establishment.
The panel is expected to submit its findings by July.
Military sources said the purpose of the panel's work it to provide objective conclusions by professional who were not a part of the operation and therefore cannot be affected by the results.
This objectivity, added the sources, would allow the panel to draw a wider range of conclusions, which may shed a different light on the events.