"Honda Racing Corporation has carried out a detailed analysis following the crash of Casey Stoner in last weekend's Suzuka 8 Hour race," said a HRC statement.
"Checking the throttle, which is a particular specification for Endurance HRC Factory bikes, and different from the standard throttle used on the Honda CBR1000RR road version, a malfunction was discovered related to the throttle cable.
"This kind of problem hasn't arisen before, however, HRC will cease using this throttle specification and will design a new one to be used for Endurance races.
"HRC would like to apologise to Casey Stoner and thank him for the effort he made in attending the Suzuka 8 Hour event."
Stoner, taking part in his first motorcycle race since leaving MotoGP at the end of 2 012, was handed the #634 Musashi machine by team-mate Takumi Takahashi near the one hour mark.
The Australian soon moved into the lead, but disaster struck shortly after at the fast right-hander leading to the hairpin. A front-wheel wobble was the first sign that the throttle had remained open and, after grabbing the clutch, Stoner ran onto the grass and fell at high speed.
The 29-year-old, who suffered shoulder and ankle fractures, soon revealed that the throttle had stuck, with Honda's initial checks suggesting it was open by 26 degrees.
WSBK star Michael van der Mark was the third member of the factory Musashi team, which was seeking its third straight Suzuka victory.
The Yamaha line-up of Bradley Smith, Pol Espargaro and Katusyuki Nakasuga went on to win the race.
