"In the Italian media two months ago, I made an open apology to Casey, what many people in MotoGP thought in the past was not true," Pernat said.
"Now we understand that the reason for many of his crashes ... the majority of people in MotoGP should now make this apology to Casey."
Ducati had jumped to the same conclusion with disastrous results, he said.
Rossi has been unable to tame the Ducati on which Stoner won the world title and is set to go through 2011 without a race win for the first time in his career.
"This was a very big mistake by Ducati, a very wrong strategy in dealing with a champion rider," Pernat said.
"To make an offer, virtually double Casey's salary, to Lorenzo who had not won a championship, while Casey was away sick, was a big mistake.
"Ducati is a proud company and they thought their bike was perfect. What they didn't understand was that only Casey could explore 100 per cent of the potential of this bike."
Pernat signed Rossi to his first factory contract in 1995 when the Italian star was 16 and was the Aprilia team boss when the Italian won the first of his nine world championships - the 125cc title in 1997.
Pernat is now a leading rider manager and media commentator and has closely followed the disaster that is Rossi's winless season.
He says the formidable rider of the past has gone missing.
"What is happening now with Valentino and Ducati is something very strange. Now he is like someone I don't know," Pernat said.
"But I know Valentino's character very well. I was first to sign him in 1995 and he has always spoken the truth, his real feelings.
"I am surprised to see him in this condition - now he is different.
"I am 90 per cent sure that Valentino will not win another world championship with Ducati.
"To be in this shit situation is very hard for Valentino, for his way of life, for his normal character and he seems different to me now," he said.
- AAP
