The Australian had left the series at the young age of just 27 following two World Championships.
Japanese magazine Riding Sport recently wrote that the Australian rider had refused to contest a Grand Prix this autumn as a wild card.
"It is true that [Honda] said they were willing to provide Stoner with a wild card if he wanted to race, but they made that proposal several months before the Austin Grand Prix", said Repsol Honda team director Livio Suppo to GPone.
"[HRC vice-president Shuhei] Nakamoto told him that if we wanted to, he could be a wild card at the end of the year in Japan or Australia, giving him some time to get prepared for it.
"However, Stoner was not interested and, since then, we have not brought it up again. I know that Nakamoto didn't mention about it during the 8 Hours of Suzuka."
When he came to Europe last June, Stoner talked about a possible MotoGP outing, stating that he would only take the place of his injured friend and former teammate Dani Pedrosa.
"Although I asked to replace Pedrosa, that doesn't mean I want to do a wild card or come back to MotoGP," he said at the time.
Stoner has no intention of contesting a race later this year, but he is scheduled to be back as a test rider in the coming weeks.
A test will be held later this autumn and Stoner will put his vast experience to use to help develop the RC213V that Honda is working on for next season.
But before this test is confirmed, Stoner's condition needs to improve. The Australian is still suffering from a badly injured ankle after he had fallen during the 8 Hours of Suzuka in July.
Stoner underwent surgery just a month ago, and is recovering from the operation.
