On the aircraft were a total of 107 Japanese nationals and their family members with foreign nationality evacuating from Oman and the United Arab Emirates.
The government also plans to bring Japanese nationals and others back from Saudi Arabia on another charter flight on Monday.
Ninety Japanese nationals and others from the UAE, where the international airport has been closed, travelled by land to Oman.
Another 84 people were evacuated from Kuwait to Riyadh, the capital of neighbouring Saudi Arabia.
Fourteen people from Tehran, Iran, 13 Japanese nationals, including embassy staff and one foreign family member arrived in Baku, Azerbaijan, early Sunday morning Japan time.
This brought the total number of Japanese nationals and others who have evacuated to surrounding countries to 188.
Japanese Prime Minister Sanae Takaichi said on X, formerly Twitter: "We will continue providing the necessary support for departures. We will remain fully committed to protecting Japanese nationals throughout the entire region, including countries surrounding Iran."
[Copyright The Jiji Press, Ltd.]