Shadowrun, like the rest of the 1980s cyberpunk genre, first based its Japanese megacorporations on the zaibatsu (with rare if any acknowledgement that the zaibatsu model had actually been replaced by the keiretsu since the 1950ies).
The comparison between European colonial empires' chartered companies is not completely off however. The economical elite of Japan were just as involved into the expansionism of the Meiji era than the European economical elite of Europe where in the colonial empires. The major difference was the Japan expansion was short-lived and never stabilized. If Japan had the time to tighten its control over its Asian holdings, it's likely the zaibatsu would have played the same role than the European chartered companies.
In any of those cases, including Shadowrun history, it's not always clear whether expansionism was initiated by the political power alone, or suggested by economical interests first.
I think it worths reminding that most of the earlier Shadowrun books, from first and second editions, described megacorporations with limited military assets, when they had any at all. Heavy gear remained the realm of national military forces. In this context, it made sense for the Japanacorps to operate under the umbrella of the Japanese Imperial Navy.
But that was how the setting was written circa 1989-1993, before Blackwater and all that - at the time, only few people knew what Executive Outcomes or Sandline were up to. A decade later, we could no longer imagine megacorporations without full-fledged military forces. The Shadowrun setting changed accordingly, which for instance resulted in the removal of the Japanese Imperial Navy from California.
