Kokubu has been a mainstay at the Japanese manufacturer for over three decades, having joined Honda in 1986, working on its MotoGP project and even briefly in Formula 1.
He did not travel to India last week and is also not present at Motegi for the Japanese Grand Prix, and will most likely be followed in a few months by Tetsuhiro Kuwata, who has a more administrative than technical role.
Kokubu's time with Honda in MotoGP is especially significant, as he was responsible for the chassis of the RC211V raced by the marque in 2003 right at the beginning of the four-stroke era of the premier class.
With that chassis, Honda won two world championships with Valentino Rossi and a third with Nicky Hayden before the RC212V was introduced for 2007 at the start of the 800cc era.
In 2008, Kokubu was appointed as project leader of the RC212V and became technical director in 2012, before taking on the role as general manager of Honda's technical and development division in 2016.
In all, Kokubu has been a significant player in Honda's MotoGP success in the modern era, being involved in all of its success with Rossi, Hayden, Casey Stoner in 2011 and with Marc Marquez from 2013 to 2019.
Kokubu's departure is significant, especially because it comes in the middle of the season, and precisely when Honda is shaking up its structure to try to get out of the complicated situation it is going through.
Honda is at the bottom of the constructors' table, where it has 123 points, two less than Yamaha, despite the fact it has two more bikes on the grid than its fellow Japanese marque and having won a grand prix earlier this year with Alex Rins in America.
The Repsol-backed factory Honda squad also sits last in the teams' standings.
As Honda evaluates a number of options to replace Kokubu, the timing of his departure comes as Marquez considers whether to honour his contract with HRC for 2024 or make a shock switch to Gresini Ducati to try to revive his fortunes.
In recent weeks it became known that Marquez had demanded Honda to make new technical hires, ideally from European manufacturers, in order to help push development of the RC213V.
This news could be seen either as an attempt to persuade Marquez - who insisted on Thursday in Japan that he is "quite sure" of his plans - to stay or to lay the foundations for a stronger post-Marquez future.
