The federation said it believed the committee would not be able to investigate the 31 May raid, during which Israeli forces killed nine Turkish nationals, in conformity with international standards and transparency, owing to the panel's make-up.
A failure to do so could risk "contributing to a culture of impunity," the open letter read.
The federation said the "highly political composition of the panel" is of the groups primary concern, adding that the nomination of outgoing President of Colombia Alvaro Uribe as vice-chair could damage its credibility and "could also affect the trust that should exist for the United Nations, and can be seen as an affront to victims."
The letter follows the appointment on Saturday of former Israeli Foreign Ministry official Yosef Ciechanover to the panel and two former Turkish diplomats.
Former New Zealand Prime Minister Geoffrey Palmer will chair the panel and will meet on 10 August.
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