Scala is angry the new Fifa council will have the ability to appoint and sack those in charge of its committees, including auditing, ethics and finance.
The council replaced the Fifa executive committee in the aftermath of a corruption scandal at the organisation.
Committees had been “deprived of their independence”, said Scala.
The Swiss added it would now be possible for the council to “impede” investigations by either dismissing committee members or “through the threat of a dismissal”.
This, he added, “undermines a central pillar of the good governance of Fifa and destroys a substantial achievement of the reforms”.
Scala has played a key role in pushing through reforms after the scandals that prompted the departures of former Fifa president Sepp Blatter and Uefa counterpart Michel Platini.
Blatter, who had led Fifa since 1998, stood down last year and was later suspended from football for six years for breaching ethics guidelines.
Platini announced earlier this week he would be stepping down after failing to have a six-year ban from football overturned by a Court of Arbitration for Sport panel.
The first Fifa congress led by new president Gianni Infantino, who succeeded Blatter in February, took place in Mexico City on Thursday and Friday.
During the congress, Fifa elected its first female secretary general with the appointment of Senegal’s Fatma Samba Diouf Samoura.
She succeeds Jerome Valcke, who in February was banned from football-related activity for 12 years. READ MORE OF THIS STORY