The series creator will serve as producer for the upcoming title, which is code-named Enders Project, reports Gematsu.
Writing on Twitter, Kojima revealed that his role is to support the team and ensure that it strikes the right balance between how the game looks and whether it will sell.
"From the start of the plan, it was clear I was just support. In reality, the game design, script, production, level design, etc. were all supervised by other staff. Even when I tried to force myself into things, I didn't have any success.
"As a producer, it's necessary to think about whether it'll sell or won't sell. You can't budget without assuming market conditions and how many will sell."
Meanwhile, screenshots of the upcoming Zone of the Enders HD Collection have been released by Konami, showing high resolution visuals and anime cutscenes.
Copyright: KonamiAnnounced at last year's E3 event in Los Angeles, Zone of the Enders HD Collection will include both Zone of the Enders and Zone of the Enders: The 2nd Runner.
It follows the recently released Metal Gear Solid HD Collection for the PS3, Xbox 360 and PlayStation Vita.
Watch gameplay footage from the original Zone of the Enders below: