Japan has the same governing problems as everywhere. Cronyism, special interests, are pervasive in the government. An embedded "ruling class" with secure salaries and pensions, following the leadership of a complicated network of "friends".
Have you heard of Japan's "roads to nowhere"? Unnecessary "infrastructure"? It was nice for well-connected Japanese construction companies who got big fat government contracts to pay workers. This produced beautifully engineered roads criss-crossing interior mountain ranges, but nobody uses them, unless it is the young practitioners of "drifting" , with souped up cars. Imagine bankrupting your country to build roads that really are a scenic race track.