But the request for two weeks off in a country where three- or four-day holidays are the norm generated such a controversy that eventually his career as a bureaucrat was sabotaged by his superiors, many of his colleagues refused to speak to him, and he was exiled to Yokohama, where he works in the quarantine section, making sure sailors do not bring cholera into the country.
Mr Miyamoto is not complaining, though. He has just written a best- seller lampooning the bureaucracy, which he accuses of institutional masochism. Called Government Office Rules, it has infuriated his bosses, pleased some of his more liberal colleagues and captivated the media at a time when change is in the air.
In the office he is still treated as the maverick who dared to speak out against official conformism and ruined his career chances. But some of the people he works with, who would perhaps like to take two weeks' holiday but dare not ask, have discreetly offered encouragement for his one- man battle against the system. 'My colleagues' attitudes began changing, particularly after the book reached 100,000 copies,' he said.
Mr Miyamoto was born in Tokyo, and after studying medicine went to the US, where he did post-graduate work in psychiatry at Yale and then taught psychoanalysis. He returned to Japan after 11 years and joined the Ministry of Health in 1986.
But within a week, he said, 'I knew I had made a mistake'. He made dinner appointments for 7pm, but no one left the office that early, and he was criticised for wanting to leave without doing the expected overtime. 'Not that they had much work to do - some were even drinking in the office, which I thought was mind-boggling. Why didn't they just go to a bar?' This was the Japanese group system, which Mr Miyamoto had forgotten after a decade in the US. The individual has to sacrifice himself to his company or employer, which is why he concludes in his book that 'good bureaucrats have to be masochists'.
Shortly after he joined the ministry, a retirement party was held for a director who had put in 35 years of service. At the party, he boasted that he had never requested any days off apart from public holidays and had accumulated two years of leave. Many applauded, but Mr Miyamoto was horrified: 'I thought he was crazy. How could he give up two years of his life?'
It was then that Mr Miyamoto decided to go on holiday, knowing his request for two weeks in one stretch would cause problems. Officially he was entitled to 23 days a year. But no one ever took their full allowance. Before the summer holiday season, a list was circulated in the office for everyone to fill in their holiday plans, and juniors were always careful not to ask for more than their superiors.
At first, his immediate boss was horrified. But after diligently plying him with sake, he gave in. The director of the section was more difficult to persuade. Mr Miyamoto had to make up a story about taking his ailing mother to southern Japan to take part in Buddhist memorial services for their ancestors, and visiting other relatives in remote rural districts. Even so, the director accused him of selfishness, causing disruption and of dishonouring his position.
Finally Mr Miyamoto got his holiday, because legally he was entitled to it. But it also put a big black mark against his chances of promotion and his superiors began hinting that he might like to resign.
The last straw, he said, was when he announced the following year that he wanted to go to Tahiti for a week: that guaranteed his dispatch to Yokohama. Mr Miyamoto's holiday battles are the starting-point for the book, which tears into a range of absurdities in the bureaucracy, such as obligatory overtime, the 'honourable' seven-day work-week, the control bureaucrats have over politics, invisible barriers erected by the bureaucracy to foreign imports as they officially work to promote imports, and so on.
Mr Miyamoto has so outraged his superiors that he is almost immune to their attempts to humble him. This year he is taking three weeks' holiday, and it seems no one tried to stop him.
'Just the other day, my director came up to me, looked at my clothes, and said: 'You are really a misfit, aren't you?' '. Mr Miyamoto had on a grey suit and a green tie with yellow dots. He said he saw nothing wrong: it was still a suit and tie, and not jeans and a T-shirt. But the director was implacable: 'You just don't look like us,' he said and stormed away.