Beijing claims Communist troops sealed victory against the Japanese in 1945 while Taiwan argues the nationalist Kuomintang (KMT) army -- which later fled to the island -- won the war.
Taiwan's objections came after a high-profile former vice president said he would attend the parade in Beijing on September 3.
"Our people should take into consideration the public's feelings and refrain from attending such activities," Presidential Office spokesman Charles Chen said in a statement.
Lien Chan, a former vice-president and chairman of the ruling KMT party, said he planned to attend the Beijing event to mark the 70th anniversary of Japan's defeat, raising eyebrows from the opposition and local media.
It was not immediately clear, aside from Lien, who will attend the parade from Taiwan, but local media said politicians, retired generals and veterans involved in the war against Japan had been invited by the Chinese authorities.
Beijing insists that Chinese communist forces led by Mao Zedong played the key role in defeating Japan.
But Taiwan wants to assert the role of the nationalist KMT army which later fled to Taiwan in 1949 under leader Chiang Kai-shek after being defeated in a civil war with the Communists on the mainland.
"The eight years of war was led by the government of the Republic of China," the defence ministry said in its statement.
"The historical truth must not be distorted and tampered with in any way."
But public sentiment in Taiwan has recently once again turned against closer ties with Beijing, with voters saying trade deals have been agreed in secret and have not benefited ordinary citizens.
Taiwan held its own parade to mark the defeat of Japan in July.
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