Like most such stories this oversimplifies a couple things in the interests of reporting the biggest, most relevant truths, which is about as good as news reporting gets. Caveats: It's usually, but not always, the foreign and male parents who are denied contact with their children. And while the Hague Convention would not get children returned if they were abducted before Japan ratifies it, it does provide for regular visitation arrangements even in those cases.
Clinton urges Japan to take action on child abduction issue
Japan Today 12/20/11 - via Kevin Brown of Children First Japan
And here, via Patrick Braden of Global Future, is video of Secretary Clinton's remarks - they don't include a lot of detail on this but she does mention that existing abduction cases, too, need to be remedied. You can skip to that part by hitting play then tracing your mouse along the timing bar and clicking at 6:00.