There is no licensing of the print or online media in Japan. However, there are a number of factors that effectively limit the freedom of many media outlets.
The kisha clubs [1], which control media access to government officials and the police, are restricted to reporters from major media organizations. The tabloid press frequently complains about those restrictions and use those restrictions as justification for their less savory reporting methods.
The libel and privacy laws are fairly strict [2, 3] and have been tightened in recent years, making publications more hesitant to report negative or personal information about individuals, including politicians. Some religious groups have used those laws to suppress negative reporting; as soon as I noticed on Friday afternoon that the mainstream media weren’t giving the name of the religious group, I wondered if fear of lawsuits was the reason. (I still don’t know.)
Extremist groups have targeted Japanese media, and have sometimes attacked [4] or killed [5] journalists, for reports that the groups didn’t like about the Imperial family or historical matters. This can make journalists hesitant to raise controversial topics.
The major newspapers are published by large conglomerates that have diverse business interests. The weekly magazines have, over the years, reported many examples of stories that were suppressed by their larger competitors because of conflicts of interest. An amusing one that I remember is when a magazine was not allowed to include the term shōgi daoshi—literally, “falling over like shogi pieces”—in their regular advertisement in a daily newspaper; they wanted to use it to describe an accident where people were crushed in and killed in a crowd, but that newspaper ran a major shogi tournament and wouldn’t allow the term shōgi to be used in a negative context. Some weekly magazines that frequently publish reports of salacious scandals about celebrities and politicians refrain from publishing similar reports about well-known writers, because their parent companies depend on work by those writers for other publications.
[1] https://en.wikipedia.org/wiki/Kisha_club
[2] https://kellywarnerlaw.com/japan-defamation-laws
[3] https://www.omm.com/resources/alerts-and-publications/alerts...
[4] https://ja.wikipedia.org/wiki/噂の眞相
[5] https://en.wikipedia.org/wiki/Tomohiro_Kojiri