This was always going to be a high-risk operation for Israel, both in terms of reputation and diplomatic repercussions.
Taking over vessels at sea is no easy task, even if the units carrying out the mission are well trained, and it is especially difficult if the people already on board the vessels resist.
The full details of what happened will emerge in time, but in political terms the damage has already been done.
The deaths threaten to make what was always going to be a potential public relations disaster for Israel into a fully-fledged calamity.
But the political ramifications could be even more serious.
A Turkish charity had a major role in organising this flotilla.
The Palestinian issue plays strongly in Turkish public opinion, where the tide is already strongly critical of Israel.
This episode will only make matters worse.
Turkish politics is changing. Groups like the military who always backed strong ties with Israel now have less political clout.
Relations between the two countries are ratcheting downwards with few pressures operating in the opposite direction to improve ties.
This incident at sea also firmly puts the spotlight on Gaza and Israel's efforts to control access to the territory.
Gaza is unfinished business with all three key players - Israel, Egypt and the United States, all happy to try to isolate the Hamas government there.
But, as aid agencies warn, this isolation comes at a price for the ordinary people of Gaza and this incident catapults their plight firmly into the spotlight.