Oliveira was in second place in the opening stages of his home Portuguese Grand Prix on Sunday when Marquez locked up his Honda and barged straight into the RNF Racing rider as both crashed out of the race.
Honda's Marquez apologised for his mistake and accepted a double long-lap penalty for next weekend's race in Argentina.
The six-times premier class champion was then ruled out of the second round in Argentina due to a hand fracture, with MotoGP saying it would carry forward his penalty to the next race he enters
"The modification of the penalty consisted of a change of criteria on when the penalty should be applied," Honda said in a statement.
"... that this modification was issued by the FIM two days after the initial sanction was final and definitive, 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."
