The Emperor went as far as he could towards expressing regret for the treatment of prisoners, but the inability of the Japanese head of state to offer the full apology demanded by the veterans meant protests are likely to continue throughout the week of his visit.
"It truly saddens me that the relationship so nurtured between our two countries should have been marred by the Second World War," said the Emperor.
"Our hearts are filled with deep sorrow and pain. All through our visit here, this thought will never leave our minds."
The Queen also referred to the pain of the conflict in the Second World War, but followed the Prime Minister in attempting to focus on the need for reconciliation, and the valuable trade links for the future between Britain and Japan.
"While the memories of that time still cause pain today, they have also acted as a spur to reconciliation," she said.
The unprecedented protest by the old soldiers in The Mall was staged to an accompaniment of catcalls, boos and the whistling of wartime anthem "Colonel Bogey".
One 83-year-old expressed his outrage about the Emperor's visit by burning a Japanese flag moments before the Queen and Emperor passed in the Irish State Coach.
Tony Blair's spokesman said there was a great deal of sympathy and understanding from the Emperor at the depth of feeling of the veteran PoWs.
They protested in service berets and medals as the Emperor travelled to the palace for his investiture with the Order of the Garter, an honour bestowed on his father and his grandfather. There were shouts of "go home" when the Emperor later emerged from Westminster Abbey after laying a wreath, but No 10 said they had demonstrated with dignity.
"I don't think it would be fair to expect him to say anything more. He is a constitutional monarch and like the Queen, he doesn't get involved in politics. We didn't expect him to make an apology. Prime Minister [Ryutaro] Hashimoto's apology and the Emperor's words have convinced the Prime Minister that they are sincere in their regrets," said the No Ten spokesman.
The veterans of the Japanese labour camps were protesting at the refusal of the Japanese government to offer more compensation, and a further apology for their inhumane treatment. But there were also civilian victims of the brutality. Sisters Elizabeth Paddon and Diana Hallward, from Devizes, Wiltshire, whose father died shortly after being released from three years' Japanese captivity in the notorious Changi jail in Singapore, waved a banner reading "The Garter is a sham".
Mrs Paddon said: "My father came home to die. We escaped from Singapore but we lost everything and my mother got compensation of pounds 48.
"We feel very bitter about this. No way should he be given the Garter. I am disgusted by Tony Blair saying we should welcome him. It is all in the name of economics and trade."
Senior members of the Cabinet, including Jack Straw, the Home Secretary, bowed their heads in greeting to the Emperor on the platform for a march past in his honour on Horseguards Parade.
The Queen told the Emperor and Empress: "I hope that you will carry away many happy memories of your stay, and that they will last through all the seasons of the years ahead, come rain or shine - for Britain is no fair-weather friend."
The protesters had ignored an appeal by Mr Blair to give the Emperor a warm welcome but the Prime Minister spent the day limiting the diplomatic damage in a series of interviews in which he emphasised the need for reconciliation. He said he wanted the rest of the visit to reflect Japan's cultural and economic links with Britain.Reuse content