The Prince is due to arrive on Saturday for a week-long tour to raise money for the Duke of Edinburgh's Award Foundation, of which he is a trustee.
But arrangements for the visit, organised from London by the Prince's own aides, have infuriated senior figures in the Foreign Office, who fear that he is being exploited by Japanese businessmen eager to gain prestige through their association with British royalty.
Inquiries have revealed some of the reasons for the diplomats' embarrassment: even though it begins in less than a week, several of the prince's Japanese hosts are still confused about arrangements for his trip, which has been fraught with last-minute cancellations, breaches of protocol and humiliating rebuffs. A number of Prince Edward's planned appearances had to be abandoned after requests to prestigious Japanese companies, including Matsushita and Suntory, for donations to the award foundation were declined.
A British embassy spokesman said he had no personal knowledge of such problems.
A proposal for a fund-raising event in Kobe, paid for by local people, with proceeds to be split between victims of last year's earthquake and the Duke of Edinburgh's charity, proved so unpopular in the devastated city that it had to be cancelled.
There are fears in the Foreign Office that the trip could further erode the reputation of the royal family in Japan, already sullied by reports of infidelity and the pending divorce of the Prince and Princess of Wales.
Particular anxiety has focused on the Japanese businessmen organising Prince Edward's visit. Their flamboyance has caused consternation among diplomats, who fear that they will undermine British credibility with the haughty Japanese establishment.
A gala fund-raising dinner in Tokyo has been organised by "Rocky" Aoki, the former Olympic wrestler and colourful founder of the Benihana chain of Japanese restaurants.
Mr Aoki became famous in Britain when he attempted to buy Red Rum, the triple Grand National winner, for pounds 500,000.
Diplomats braced, page 12