The statement followed a story in yesterday's Times which claimed that the Duke had privately expressed reservations about the decision.
In a statement yesterday a Buckingham Palace spokeswoman said: "The Duke has not expressed any view, privately or publicly, over the award of the Order of the Garter to the Emperor of Japan.
"He is well aware of the painful memories which the War caused to people, both from his own wartime experiences and from meeting veterans and ex- prisoners of war over the years since.
"For very many years, Prince Philip has worked for reconciliation and for a greater understanding between the two countries."
It is understood that the Duke has not ruled out making a complaint over the report to the Press Complaints Commission.
Survivors of Japanese prisoner of war camps yesterdaycondemned the decision to confer the award on the Emperor of Japan. Members of a former civilian internees group met in central London to condemn the award of the Order of the Garter to Emperor Akihito. They also demanded an urgent meeting with the Prime Minister before the Emperor's visit to Britain later this month.
The campaigners want a "meaningful apology" and compensation from the Japanese government for their suffering during the Second World War. The outcry came after the Duke of Edinburgh's denial.
The Japanese head of state will receive the award on his visit, which begins on 26 May.
Keith Martin, chairman of the Association of British Civilian Internees - Far East Region, said yesterday: "I think the Garter is an order too far.
"It seems an insensitive thing to do. Here is an order that was given to people like Winston Churchill, Montgomery and other great British leaders. What has the Emperor done that is chivalrous?"