The good news: Most if not all of the major national newspapers in Japan run their own web site where they reproduce their content online.
The bad news: Unlike the UK and USA at least, almost all the free content (which represents just a small percentage of the total story count in the paper newspaper) is heavily-edited down to just two or three paragraphs reporting the facts, and often expires after a few weeks or even days. Furthermore, a noticeable percentage of the articles are from wire copy, so different sites end up reporting the story in rather similar ways.
What this means: A report that "Story X or View Y cannot be found through Japanese Google News Search" means very little, especially as the context is usually "…thus Team Japan is covering it up!". Newspaper readership is still around 70% even for internet users, so the publishers see no reason to give their product away for free. Thus, newspaper spin and analysis are difficult to find online, so someone relying purely on reading these free sites will be woefully uninformed regarding what is happening in the country.