Thailand currently holds the presidency of the human rights council.
De Silva is a former chief war crimes prosecutor at the UN-backed special court for Sierra Leone. Hudson-Phillips is a former judge at the International Criminal Court and Shanthi Dairiam is a women's rights activist.
The team is expected to travel to Israel, Turkey and Gaza next month to interview witnesses and gather information. It will report its findings in September.
It is unclear whether Israel will co-operate with the inquiry; Israel has said that its soldiers acted in self-defence, and has rejected calls for an international investigation.
An internal Israeli army inquiry completed earlier this month recommended no disciplinary action against senior officers, and concluded that "the use of live fire was justified" on board the Mavi Marmara.
A separate civilian panel, chaired by former Israeli supreme court judge Jacob Turkel, is also investigating the raid.
Israel's defence ministry announced on Friday that it would return seven ships from the flotilla to Turkey, including the Mavi Marmara.
The ships have been sitting in Israel's Ashdod and Haifa ports for more than a month, despite repeated requests from the Turkish embassy that the ships be returned.
The ministry said it will co-ordinate with Turkey to arrange for the return of the ships, a process which could take several weeks.