MotoGP championship leader Rossi has been sanctioned for the incident that saw Spain's Marquez crash in Sepang and the Italian will start from the back of the grid in Sunday's final race of the season in Valencia.
Rossi has appealed the decision and a hearing will be held 48 hours before Sunday's race, which could see Rossi's seven-point lead over Spanish rival Jorge Lorenzo come under threat.
Honda on Monday claimed technical data from Marquez's bike proved that Rossi kicked him as they jockeyed for position on a bend in Sepang.
But Yamaha issued a statement on Tuesday which refuted the claims, underlining the fact they were not proven by race officials in Malaysia: "Yamaha would like to express its disagreement with the words that have been used to report on the incident between riders Valentino Rossi and Marc Marquez," said the statament.
"Both press releases included words that accuse Valentino Rossi of kicking Marc Marquez's bike... that is something not proven by the investigation of the Race Direction.
"We therefore reject the wording used in the said published statements that do not correspond with the findings of the Race Direction."
The Italian MotoGP legend's actions have caused widespread outrage in the Spanish media. But Rossi has denied kicking defending champion Marquez, claiming he is the victim of a Spanish plot.
He accuses Marquez of pursuing a "dirty game" with the express intention of helping compatriot Lorenzo win the title, claiming Marquez conspired to help Lorenzo win points in Australia.
Japanese constructor Honda on Monday claimed their technical data proves Rossi kicked Marquez's machine.
"It is clear that Valentino intentionally pushed Marc towards the outside of the track, which is out of the rules, therefore Marc had no other option other than to run wide," said Honda's vice-president Shuhei Nakamoto.
"The data from Marc's bike shows that even though he was picking up the bike trying to avoid contact with Valentino, his front brake lever suddenly received an impact that locked the front tyre, which is the reason for his crash.
"We believe that this pressure was a result of Rossi's kick."
Spain's secretary of state for sport, Miguel Cardenal, told Spanish media that he hoped "fair play" would rule at the MotoGP season finale on Sunday.
Rossi, seeking a record-equalling eighth premier class title, heads to Valencia on 312 points with Lorenzo on 305.
Yamaha said the best way to draw a line under the "unfortunate affair" was to try to win what they hope will be a "memorable final race" in Valencia.
"Yamaha has no wish to enter into further discussion regarding this unfortunate affair and our desire is to conclude the 2015 MotoGP season in the best possible way," the statement added.
"We go to Valencia with the clear intention of trying our best to win what we hope will be a memorable final race with all riders and teams competing in an exemplary sportsmanlike manner befitting the top category of motorcycle racing."