The total of 3.08 million represented an increase of 69.5% from March 2023 and a 11.6-% gain compared to March 2019 before the pandemic battered global tourism, the Japan National Tourism Organization said.
"This was the highest single month on record and the first time the number of visitors exceeded three million," the government agency said.
On top of generally rising tourism demand, factors included the spring cherry blossom season and the Easter break helped boost visitor numbers.
Record numbers arrived from overseas including from India, Germany, Taiwan and the United States.
Tourism to Japan has been booming since pandemic-era border restrictions were lifted and the government has been working hard to boost visitor numbers.
But this has not been universally welcomed, including in Kyoto where locals have complained of snap-happy tourists harassing the city's immaculately dressed geisha.
These "women of art" work for a living -- as they have for centuries -- in teahouses in Kyoto's picturesque Gion district where they perform traditional Japanese dance, music and games.
This summer, hikers using the most popular route to climb Mount Fuji will be charged $13 each, with numbers capped to ease congestion and improve safety.
The mayor of the western metropolis Osaka has also said he is considering charging a new fee to foreign tourists, separate to an existing tax on hotel stays.