The 39-year-old had won both races on the Ryan Farquhar-prepared J McC Roofing Kawasaki by a wide margin, but his disqualification means Frenchman Pierre Yves Bian (VAS Paton) is the winner of race one, with Joe Loughlin from Castleblayney declared the winner of race two.
Prior to the disqualification, Farquhar revealed that a protest had been submitted over a technical infringement.
He said: “A protest has been put in over a technicality to do with a fairing bracket.
“I fought my corner because you’re allowed to change the bracket, and it was done for safety. They weren’t going to let Richard out in that race and said he had been disqualified, but I put an appeal in against it and that’s where we are at the moment.
“The bike went through scrutineering all week and it’s visible for everyone to see – it’s only a bracket holding the fairing on and there’s no performance advantage gained whatsoever,” he added.
“But this has been happening to me for years and I’m not surprised really – it’s just sour grapes.”
A statement from the NW200 organisers said: "The results of both the Milltown Service Station and JM Paterson Supertwin races have been amended following the exclusion of Richard Cooper’s JMC Roofing Kawasaki because of a modification to the machine’s frame which is deemed to be against the rules by the stewards of the meeting.
"They have excluded the machine from the results which means Richard Cooper is now disqualified as the winner of both races.
"Pierre Yves Bian (VAS Engine Racing Paton) and Joe Loughlin (ILR/Coverdale Paton) are now the race winners."