Repsol Honda alleged the International Motorcycling Federation (FIM) has "violated" the team's rights after its decision to uphold Marc Marquez's ban beyond the Argentina Grand Prix.
The six-time MotoGP champion suffered a fracture to the first metacarpal bone in his right hand in Sunday's Portuguese Grand Prix.
That was after a crash with Miguel Oliveira at Turn 3 early in the race, with Marquez found guilty of irresponsible riding in Portimao after both riders were unable to continue.
The Spaniard was handed a double long-lap penalty and the FIM confirmed Marquez will serve the sanction when he next features after Honda announced he will miss the next race due to a hand operation.
Honda have contested the FIM's ruling, questioning the merits of changing the penalty two days after the initial sanction.
"The modification of the penalty consisted of a change of criteria on when the penalty should be applied," Honda said in a statement on Wednesday.
"This modification was issued by the FIM two days after the initial sanction was final and definitive, and is not in line with the current regulations of the FIM for the MotoGP World Championship.
"The Repsol Honda Team intends to use all the means of recourse to defend its rights and legitimate interests, which it considers violated as a result of the latest resolution adopted, and in particular has duly submitted an appeal before the FIM Appeal Stewards."
Japanese team Honda have opted to go to the Termas de Rio Hondo Circuit with just one rider, despite having test rider Stefan Bradl available.
Joan Mir will step up in the absence of Marquez as the 2020 world champion prepares for his second race in the team's colours on Sunday in Santiago del Estero.