FIFA's independent audit and compliance chairman Domenico Scala resigned Saturday in protest at a congress decision he says "undermines" reforms at football's scandal-hit governing body.
His resignation follows a decision by the FIFA congress Friday in Mexico City to allow its new-look council the right to appoint and dismiss members of key control bodies including the governance and compliance committees.
The Swiss-Italian said the move meant the council could now prevent investigations against individual members or that governance committee members could be silenced by the threat of dismissal.
The control organs were effectively "deprived of their independence and threaten to be agents of those who should actually monitor them," he said.
"I am dismayed about this decision, since a central pillar of good governance of FIFA is undermined and a major achievement of the reforms is nullified.
"For this reason, I hereby declare my immediate resignation as chairman of the audit and compliance for FIFA."
FIFA said in a statement Scala had "made unfounded claims which are baseless" and "misinterpreted the purpose of the decision" taken by the 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," the statement said.
"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."
Current deputy chairwoman Sindi Mabaso Koyana of South Africa will be acting chair pending the appointment of a successor to Scala.
Scala's resignation is a setback for new FIFA president Gianni Infantino, elected in February with the commitment to bring in radical reforms at a governing body mired in various corruption scandals under predecessor Joseph Blatter.
Infantino however defended the decision to allow the new council the right to appoint and dismiss members of the control committees.
The move did not contravene the independence of the watchdog committees and would provide "flexibility" for the council for the next year "to dismiss and appoint members if the council feels it is needed," he said.
Scala said he had worked on reforms for FIFA since Blatter announced last June he would be stepping down, leading to the extraordinary congress in February approving a "pioneering package" which paved the way for "a credible future" for FIFA.
His resignation should be "a wake up call" and "strengthen the backs to all those who have been committed to the implementation of the reforms."
At Friday's congress, FIFA appointed its first female and non-European secretary general in the Senegalese UN official Fatma Samoura. In its statement Saturday, FIFA said this was evidence that it was "focused on reform and the path forward."
Infantino also declared FIFA's corruption problems to be in the past.
"Nobody can change the past but I can shape the future," he said. "FIFA is back on track. So I can officially inform you here, the crisis is over."