Netanyahu's testimony lasted for more than four hours on Monday.
Ehud Barak, the defence minister, is scheduled to testify on Tuesday and General Gabi Ashkenazi, the army chief of staff, will appear on Wednesday.
Ashkenazi is the only member of the Israeli army scheduled to testify.
Netanyahu blamed the Turkish government for failing to "halt" the flotilla, which was organised by a Turkish group, IHH.
"Despite our diplomatic efforts, the Turkish government did nothing," he said.
"[It] did not consider the confrontation between Turkish activists and Israel to be against its interests."
Netanyahu also maintained that Israel had the right to search for weapons on board the flotilla.
He accused Hamas of "stockpiling weapons" in Gaza, and denied that Israel's blockade of Gaza created a humanitarian crisis.
"Elements hostile to Israel used the bogus rationale of a humanitarian crisis in order to try to break the naval blockade," he said.
Navi Pillay, the United Nations' human rights chief, called the blockade "devastating" last year.
A 2008 report from the International Committee of the Red Cross found that 70 per cent of Gaza's population suffered from food insecurity; Gaza has less than one-fourth the hospital capacity of Israel; and four out of five Gazans depend on external aid to survive.
The Israeli government did not find any weapons intended for use by Hamas or other groups when it searched the ships after the raid.
Netanyahu refused to answer several questions in public, including not naming the officials who talked with the Turkish government prior to the raid.
Nor would he say if the Israeli government considered a non-military approach to stopping the flotilla.
After the public session recessed late on Monday morning, additional testimony to the panel continued behind closed doors.
Eight Turkish and one Turkish-American activist were killed in Israel's May raid on the flotilla.
The Israeli government insists that the raid was consistent with international law, and that the soldiers who boarded the ships only opened fire after they were attacked.
Activists on board the Mavi Marmara, the lead vessel of the flotilla on which all the activists were killed, claim they were fired on first.
The Israeli army has already conducted its own probe of the raid, which concluded that the use of live fire was justified.
Turkey's state prosecuters launched their own investigation into the incident on Monday, beginning with a tour of the Mavi Marmara.
The ship arrived in the southern Turkish port of Iskenderun on Saturday after being released by Israeli authorities.
A separate United Nations panel is expected to begin its probe into the raid later this week.
Israel threatened to pull out of the UN inquiry if its soldiers would be called to testify.
"Prime Minister Benjamin Netanyahu makes it absolutely clear that Israel will not cooperate with and will not take part in any panel that seeks to interrogate Israeli soldiers," the Israeli government said in a statement on Monday.
Ban Ki-moon, the UN secretary-general said international investigators made no agreement with Israel not to call soldiers to testify.
"There was no such agreement behind the scenes," Ban said at a news conference on Monday.