Freelance reporter Yuki Kitazumi was arrested last month and charged on Monday—World Press Freedom Day—with spreading fake news, according to a report by Kyodo news agency.
He is one of 50 journalists currently held in Myanmar as part of the junta's crackdown on widespread protests against the February 1 coup.
The country has been in turmoil since civilian leader Aung San Suu Kyi's government was ousted, with more than 750 people killed as security forces struggle to quash near-daily demonstrations against their rule.
Kyodo cited an unnamed Japanese embassy official saying Kitazumi had no health problems, despite spending several weeks in Yangon's Insein prison, which has a long and unsavoury reputation for holding political prisoners.
Kitazumi has been in custody since April 18 — the second time he had been arrested since the coup.
In February, he was beaten up and briefly held during a crackdown on protesters but was later released.
Japan, for years a top aid donor to Myanmar, has been pressing for his release.
"Naturally, we will continue to do our utmost for the early release of the Japanese national being held," Foreign Minister Toshimitsu Motegi told Japanese journalists during a trip to Britain, according to national broadcaster NHK.
A total of 766 civilians have been killed in the military crackdown on protests, according to the Assistance Association for Political Prisoners (AAPP), a local monitoring group.
As well as arresting journalists, the generals have also sought to clamp down on news of the crisis by shuttering independent media outlets and throttling internet speeds.
The AAPP says there are 50 journalists in custody at the moment, 25 of whom have been prosecuted, while arrest warrants are out for another 29.
Despite the dangers, protesters continue to take to the streets, with early-morning demonstrations on Tuesday in the second-biggest city Mandalay, as well as northern Kachin state.
The military has defended its seizure of power, pointing to fraud allegations in the November election, and condemned protesters as rioters and terrorists.
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