The carrier said the move was a result of the retirement of six B747-400 aircraft as well as the continued yen devaluation and average fare decline with lower fuel surcharge.
The change will come into effect from October 23.
Aside from Saipan, Hawaii will also see a reduction of Delta flights starting in late October.
According to arrival statistics provided by the Marianas Visitors Authority, 2015 has seen a reduction in Japanese arrivals every month compared to the previous fiscal year.
For August this year there were 6,991 Japanese arrivals compared to 12,362 during the same period last year.