TI had been invited by Fifa to take part in an external panel to advise on reforms within the organisation, but has now decided to end the collaboration.
Transparency International stressed that Mark Pieth, an external expert who will oversee Fifa's reform plans, should not be paid by the organisation itself in order to guarantee his independence, but this recommendation was ignored.
"We believe that someone paid by Fifa cannot be a member of the independent commission overseeing reforms," TI's sports adviser Sylvia Schenk told the Press Association Sport news agency.
"He has a contract with Fifa so he is not independent in that sense."
TI's proposal to re-examine old scandals was also declined by Pieth.
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