The commission, which will work under the prime minister's office, will "investigate the attack and the treatment the activists faced" before writing a report on its findings, the ministry said in a statement.
The report will be presented to the international inquiry set up by the United Nations earlier this month to look into the Israeli operation, it added.
The Turkish commission will include bureaucrats from the foreign, justice, interior and transport ministries as well as officials from the maritime agency.
The statement did not say when the commission would finish its report.
The May 31 raid by Israeli commandos on the flotilla of six ships in international waters triggered international criticism of Israel and plunged bilateral ties with Turkey into a crisis.
In June, Turkish prosecutors also launched an investigation against top Israeli leaders, which could result in them pressing charges, among them murder, injury, attacking Turkish citizens on the open seas and piracy, according to press reports.
Israel has set up two internal investigations into the raid, but Turkey has dismissed them, expressing doubt over their impartiality.
Ankara says it is confident the UN commission will shed light on the incident, but Israel has threatened to pull out of the probe if the UN commission insists on grilling Israeli soldiers.
Israel says its commandos resorted to self-defense after they came under attack from the activists on board. The activists say the soldiers fired as soon as they boarded the vessels.
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