FIFA has accused Domenico Scala of making "unfounded claims" as it accepted the auditing and compliance chief's resignation.
Scala announced his departure on Saturday after expressing concern that the autonomy of FIFA's independent committees was being eroded by new powers given to the FIFA Council.
A resolution, passed by 186 votes to one, gave the new body - a replacement for the Executive Committee - the power to appoint or dismiss any office holders of its independent bodies.
Scala said the new rule "undermines a central pillar of the good governance of FIFA and it destroys a substantial achievement of the reforms".
A FIFA statement read: "FIFA accepts Domenico Scala's resignation as Chairman of the Audit and Compliance Committee with immediate effect.
"FIFA regrets that Mr. Scala has misinterpreted the purpose of the decision taken by the FIFA Congress. The decision was made to permit the Council to appoint members on an interim basis to the vacant positions of the new committees so they can start fulfilling their roles as part of the ongoing reform process until the next FIFA Congress in 2017. In addition, the measure allows for the swift removal of members who have breached their obligations.
"The Council fully respects the independence of the Audit and Compliance and the Ethics committees, and any suggestions to the contrary are without merit.
"Mr. Scala has made unfounded claims which are baseless. FIFA is focused on reform and the path forward as evidenced by the appointment of a new FIFA Secretary General.
"Pending the appointment of a new Chairman of the Audit and Compliance Committee, current Deputy Chairman Sindi Mabaso Koyana will serve as acting Chairman.
"The appointments of all members of the FIFA Audit and Compliance Committee and FIFA's judiciary bodies are subject to strict eligibility checks by the independent FIFA Review Committee. The Congress elects the members of the Review Committee.
"Former European Court of Justice Advocate General Miguel Poiares Maduro, former Indian High Court judge Mukul Mudgal and former Sporting Cristal President Felipe Cantuarias Salaverry will form the first independent Review Committee. This mechanism is designed to protect the organisation against any conflict of interest in the approval of any appointments to the key committees and bodies."
Fatma Samba Diouf Samoura was appointed secretary general on Friday.