Nepal and Japan have increased the number of flights from twice weekly to 14 weekly with any type of aircraft on a reciprocal basis.
The decision was taken after the two nations revised their bilateral air services agreement (ASA).
Nepali carriers are now allowed to fly to various airports in Japan, except Tokyo International Airport (Haneda Airport), Tourism Ministry Secretary Krishna Prasad Devkota said.
"Due to traffic congestion at Haneda Airport, Japan said it was difficult for them to allocate a slot," Kathmandu Post quoted Devkota as saying.
As per the old ASA, which was signed on February 17, 1993, Nepal airlines could only operate 400 weekly seats or two weekly flights out of a single airport. The deal followed negotiations lasting nearly 12 hours, as per Kathmandu Post.
The move to amend the 25-year-old ASA comes after the national flag carrier announced the plan to spread its wings to Japan.
Nepal has signed bilateral ASAs with 38 countries, since 1963.