China accused Tokyo of poisoning already strained Sino-Japanese relations by allowing Taiwan's former president to visit Japan.
Tokyo said on Thursday that the 81-year-old Lee Teng-hui was granted a tourist visa and will come to Japan this month. Mr. Lee is a vocal proponent of Taiwanese independence.
China says Japan's decision strengthens Taiwan's move towards independence.
Chinese Foreign Ministry spokesman Liu Jianchao urged Japan to reverse course. Mr. Liu said Mr. Lee is the mastermind behind Taiwan's independence movement and China hopes, even requires, Japan to cancel its decision.
China considers Taiwan its territory, although the island has been governed separately since Nationalists fled there after losing a civil war to the Communist Party in 1949.
Beijing opposes moves that might reinforce impressions of Taiwanese independence, including visits by Taiwanese leaders to other countries.
Mr. Lee left office in 2000 but remains active in local politics and is a fierce critic of China's Taiwan policy.
Three months ago, Tokyo denied Mr. Lee a visa but officials say this latest application was granted because the former president promised he would not engage in politics during his visit.
Japanese Foreign Minister Nobutaka Machimura said Thursday the issue is not important as Mr. Lee is making a private trip. He said he does not think the visa issue will hurt relations with China.
Mr. Lee's visit is the latest in a series disputes souring relations between the two Asian leaders.
The countries have squared off over control of a small group of uninhabited islands in the East China Sea. The islands sit near a possible underwater gas field.
In November, a Chinese nuclear-powered submarine passed into Japanese waters. Beijing later apologized for the incident.
Last week Japan labeled China a national security threat and said it will start to shift its defense focus from Russia to China.