The 19-year-old Briton took part in the Suzuka pre-season test earlier this month, ending up with the eighth-best time.
However, earlier this week, ThreeBond issued a brief statement on its Facebook page stating that it had been forced to axe Ahmed due to a "major problem" related to his contract.
It added that it expects to name a replacement driver for the Briton soon, and also clarified that Ai Miura's place in the team is unaffected.
TOM'S driver Ritomo Miyata - runner-up behind the dominant Sho Tsuboi in last year's standings - topped the Suzuka test by less than a tenth of a second ahead of one of Ahmed's rivals from European F3 last year, Sacha Fenestraz.
Suzuka plays host to the opening round of the new season on April 20-21.