One of the major reasons given for the decline of the Japanese economic miracle is summed up in the link below. The link discusses the pros and cons of the Japanese agency formerly known as MITI. MITI was given much of the credit when Japan was riding high but many scholars now argue that it was to blame for Japan's "fall." They argue that having the state try to decide which industries should succeed is inherently inefficient. They argue that MITI made too many mistakes that did not allow Japan to really progress.
Another commonly advanced reason is Japan's corporate culture. This argument asserts that Japan's business culture is too conservative to succeed in today's world. It points to things like the alleged Japanese tendency to have firms that guarantee lifetime employment and the practice of having advancement be strictly by seniority. These sorts of practices make Japan's corporate culture hidebound and inefficient.
These are two of the causes most commonly cited as reasons for the decline of Japan's economy.