The developer of the P2P software has also had his home searched by police, according to a report in the Mainichi Daily.
There are around a quarter of a million users of the supposedly anonymous file-trading network, called Winny, which rides on the more well-known Freenet network.
Such networks differ from other file trading software, such as Kazaa, in that they claim to be able to hide the Internet Protocol (IP) addresses of users. It is not known how the police managed to track down the two users, or why criminal action is being taken against them. In other countries, P2P users have been hit with civil lawsuits instead.
The creator of Freenet, Ian Clarke, has cast doubt on whether Winny uses Freenet's full identity-cloaking features or its cryptography, according to a report in New Scientist.
Freenet is an open-source project and is the most prominent of a growing number of projects aimed at giving people the ability to communicate online without being tapped, traced or monitored.
The software marks an attempt to create a network that exists as a parallel Internet, where content of any kind can be uploaded and downloaded without any way to track who created a given "site".
Unlike other peer systems, Freenet has a built-in method of pushing content between different computers, so that a given file can migrate around the network between different people's hard drives until it is stored near regions where it is most often used.
The arrested are two men, aged 41 and 19, said the Mainichi Daily report. Among other charges, the older man is accused of sharing the Hollywood movie "A Beautiful Mind" while the teenager is being held for making the game Super Mario Advance available online.
Several companies, including game maker Nintendo, are pressing charges against the pair. This is the first known case of legal action being taken on users on anonymous file-sharing networks.
In Korea and Taiwan, lawsuits have been filed against users of P2P networks. A copyright body in Taiwan is suing three users of file sharing networks, while in Korea recording companies are threatening to do the same.
In both countries, creators of file sharing software have been brought to court, but defendants are arguing that they are not responsible for what people choose to share. Both cases involve homegrown P2P networks sharing local-language music.
In Taiwan, the International Federation of the Phonographic Industry (IFPI) has sued three P2P users who are said to have shared files on the locally-popular Kuro and Ezpeer networks.
Unlike internationally popular networks such as Kazaa, both Taiwanese services are fee-based.
The Recording Industry Association of Korea (RIAK) is said to be mulling suing end users of free-use P2P software Soribada.
Soribada's 4.5 million users have lost the recording industry millions in revenue, claimed the RIAK. The makers of the software have been slapped with a $16,300 (£9428) fine, despite claiming that they are not responsible for the actions of its users.
In the US, the Recording Industry Association of America (RIAA) has targeted hundreds of P2P users for legal action.
There is some evidence that the controversial RIAA lawsuits against ordinary computer users are making a dent in the file-swapping world. According to Web analysis firm Nielsen/NetRatings, weekly usage of the Kazaa software in the United States plummeted from a high of 7 million people in early June to just 3.2 million people in late October.
News.com's John Borland contributed to this report.
