"My Honda is more competitive than me at the moment. And yes, the ankle felt worse after three days' ridding,'' Stoner said after last Sunday's race in Japan.
"I've been icing it and I'll ice it again and try to rest it as much as possible to be as good as I can for Malaysia which is going to be a hot weekend.''
The Malaysian GP is the second of a triple-header that includes next week's Australia GP at Phillip Island which is Stoner's farewell home race before retirement.
Stoner will have had just five days' recovery before being back on track for opening practice on Friday at the Sepang circuit in Malaysia. He just hopes it is enough.
He says three races in 14 days is a massive challenge in his condition as he prepares for retirement after the Valencia GP in November.
"Physically, Japan and Malaysia have always hit me pretty hard so it's not the way to come back after a long break so three races back-to-back is going to be very tough,'' Stoner said.