"We have caused tremendous damage and pain to many countries, particularly the Asian people, during the war. We deeply regret that and sincerely mourn for those who were sacrificed and their relatives," Noda said. "We will not repeat the same mistake."
Emperor Akihito, whose father made the unprecedented 1945 national radio address announcing the war could not be won, also offered prayers for the dead.
Simmering tensions between Japan and its neighbors have threatened to boil over in recent weeks.
Tokyo was angered by a recent visit by South Korean President Lee Myung-bak to contested islands in the Sea of Japan, called Takeshima in Japanese and Dokdo in Korean. The visit was seen by many as an attempt by Lee to play up anti-Japan sentiment ahead of elections later this year.
A group of South Korean protesters swam across the sea to the island Wednesday, while a shipload of activists from Hong Kong was heading to another set of disputed islands in the East China Sea claimed by Japan, China and Taiwan.
The Hong Kong boat briefly entered the territorial waters around the islands, called Senkaku in Japan and Diaoyu in China, as Japanese Coast Guard patrol vessels warned against entry, Chief Cabinet Spokesman Osamu Fujimura said. The Prime Minister's Office also set up a taskforce in case of emergency, he said.
In a ceremony celebrating Japan's defeat, Lee on Wednesday condemned Japan for forcing thousands of Korean women into sexual slavery to Japanese soldiers during the war.
Historians say up to 200,000 "comfort women," many of them also from China and the Philippines, were forced to provide sex to Japanese soldiers at military brothels during the war. Japan has apologized and initiated a private fund as a way to pay the women without providing official compensation, but many of the women rejected the offer, demanding a formal apology and state compensation.
On Tuesday, Lee said Japan's emperor should apologize to Koreans who died while fighting for their liberation from Japan if he wants to visit South Korea.
Noda called Lee's remark "puzzling and regrettable."
Japan lodged a protest to South Korea over Lee's emperor remark, Foreign Minister Koichiro Gemba said, denying Japan has ever discussed with South Korea a visit by the emperor.
"Making words and actions that only inflame nationalism at a time we need to respond calmly would only go against South Korea's own interest," Gemba said. He also said Japan is considering bringing the island dispute to the International Court of Justice.
While Japan routinely apologizes for its wartime actions, its politicians often anger countries that bore the brunt of its colonial aggression by visiting the Yasukuni Shrine, a Japanese memorial honoring the war dead including top war criminals.
Two Japanese ministers from Noda's Cabinet -- Jin Matsubara, head of the National Public Safety Commission and Yuichiro Hata, the transport minister -- and dozens of national lawmakers visited the war shrine on Wednesday.
Matsubara said he visited Yasukuni in his private capacity.
"I was only truthful to my own principle as a Japanese citizen," he said.