The Ducati has had four major revisions to the chassis this year to try fix Rossi's problems which he continues to say relate to the vague feeling of the front-end.
Two races ago, at Aragon in Spain, Rossi ditched the carbon fibre frame which Stoner had used in favour of a new aluminium frame which he says is better, but not much.
Stoner is puzzled by Rossi's issues with Ducati but admits his new Honda is much easier to ride.
Last year, Stoner won three of the last five races on the Ducati and claims it was still a winning bike at the beginning of this season.
But Rossi has a different style, with smoother corner lines that demand precise steering and front feel and he cannot ride the set-up which Stoner used to great success at Ducati.
"Stoner modified the setting and he rode like a devil and he made great results last year with nothing to lose and he raced all or nothing," Rossi said.
"It is not a criticism of Casey because, at this moment, I am not able to do like him on the Ducati."
Stoner says it is a mystery to him why Rossi is struggling.
"I had four chassis in four years at Ducati. Rossi's had that many changes this year and Ducati spent a lot of money for no reward - there is something strange there. Something should have worked by now."
The latest changes include modifications to Rossi's riding position on the bike and, at the last race in Motegi in Japan, this produced some better feeling.
"At recent races, I was bit unbalanced on the bike, not in my natural position, but now I can ride better," Rossi said. "When I can ride in my normal position, I can go faster.
"But the problem is we work a lot at Ducati but don't fix a lot. Perhaps we do not fully understand the problem.
"It is maybe a problem to match between me and the bike and I'm not sure if, with this new chassis, the situation improves or if it really is a problem of the material.
"It is very difficult to say. Unfortunately, I am not an engineer and I don't know. This answer must arrive from Ducati."
- AAP
