The two-time world champion trialled a new frame and engine aboard the manufacturer’s current RC213V bike and prototype machine for 2014.
Unlike previous tests the retired two-wheel ace has undertaken for Honda this year, Stoner enjoyed mostly clear conditions at Sugo circuit.
“It’s been quite a good three days and we got a lot of track time considering it gets dark and cold here quite quickly,” he said.
“We had a busy test schedule based on the current 2013 bike and an updated version of the 2014 bike. Both have some very positive aspects and we’re just trying to get a better understanding of them.
“It was a little tricky to get a true feeling here in Sugo as we had no comparison — with it being the first time we’ve ridden here.
“All in all it was a good test and the first time we’ve not been interrupted by rain.”
Stoner became the youngest ever inductee into the MotoGP Legends Hall of Fame at Phillip Island a fortnight ago, when he was also granted a lap of honour with fellow Australian motorcycling greats Wayne Gardner and Mick Doohan.
He used the occasion to reiterate he had no desire to return to MotoGP, amid speculation his frequent tests with Honda would lure him out of retirement.
“Honestly, this is my feeling: I have no wish to return, especially at this moment. I’m happy to just watch from the sidelines,” he said.