Ito will race a fourth factory bike alongside Casey Stoner, Andrea Dovizioso and Dani Pedrosa, while Akiyoshi will be placed with LCR Honda, which will still field regular rider Toni Elias.
The additional entries will give Honda a record eight-bike presence in MotoGP for the Motegi round.
A statement from Honda said Ito and Akiyoshi's entries were a gesture of support to those affected by the earthquake and tsunami in Japan in March. The Motegi race was put back six months due to the after-effects of the disaster.
"Through their participation in the Japanese Grand Prix, HRC hope to bring courage and show support for the East Japan area," said the statement.
Both riders have mainly raced in Japanese Superbikes in recent years. Akiyoshi has made a number of substitute appearances in MotoGP, most recently riding for Gresini Honda at Assen this year when Gresini's Hiroshi Aoyama was seconded to the factory team to deputise for the injured Pedrosa.
Ito was a MotoGP regular with Honda from 1993 to 1996, taking six podium finishes during that period and fifth in the 1995 title race. His last MotoGP appearance came on a Pramac D'Antin Ducati in the 2007 Japanese GP.