The numbers of visitors from Hong Kong and Thailand came to 55,400 and 29,300, also all-time highs for the reporting month, the agency said.
About 18,873 Thais travelled to Japan in September last year and 23,900 visitors from Thailand went to the East Asian country in August this year.
Almost 256,000 Thais went to Japan from January to August this year and the number jumped after Tokyo waived visas for tourists staying for up to 14 days since July.
The Japanese government has dismissed rumours that it plans to halt visa-free entry for Thai tourists at the end of this year, the Japanese embassy in Thailand said in a statement on Tuesday.
The number of South Korean visitors fell below 200,000 for the first time this year, apparently due to concern over reports about leaks of radiation-contaminated water from the crippled Fukushima Daiichi nuclear power plant, JNTO officials said.
The September total of South Korean visitors came to 164,500, up 12.9%. But the growth marks a slowdown from year-on-year growth rates in the January to July period that ranged between 28.6 and 45.5%.
The September growth also compares with the previous month's 6.9% rise, which represents the slowest rate of growth seen this year.
The Japanese government is worried that the concerns among South Koreans may hamper efforts to clear its goal of pushing up the annual number of foreign visitors above 10 million.
The number for the first nine months of this year totalled 7.73 million of which South Koreans accounted for 25%. As no sharp recovery is expected in the number of South Korean visitors, the organisation plans to encourage people in Southeast Asian countries to visit Japan during the Christmas holiday season.
In the reporting month, the highest number of tourists came from Taiwan at 206,800, also an all-time high for the month. Taiwan clinched the top slot from South Korea, which moved into second place.
China was in third place with 156,300 visitors, up 28.5% and also an all-time high for the month.
The Chinese number marked the first rebound in a year after year-on-year changes in the number of Chinese visitors remained in minus territory since last October amid a strain induced last year by the Japanese government's move on the main part of the China-claimed Senkaku Islands in the East China Sea. The islands are known as Diaoyu in Chinese.