The Japanese visa is being granted solely on humanitarian grounds, and Lee will be limited to seeking medical treatment for his heart condition, officials said.
China warned Japan against granting Lee an entry visa, regarding the island democracy as a renegade province and any international recognition of it as an affront. The sides split amid civil war in 1949.
Lee, 78, is vilified by China for trying to break Taiwan out of diplomatic isolation during his rule.
"Mr. Lee is a very influential person politically," Japanese Foreign Minister Yohei Kono said. "I think we are about to enter a difficult period in our diplomatic relations with China."
Japan, like most countries, recognizes the communist government in Beijing as the only legitimate ruler of China, and Kono said allowing Lee to visit does not reflect a change in policy.
The United States, which also follows a "one China" policy, issued Lee a tourist visa.
A U.S. official said Lee planned to travel April 30 to May 6.
Reeker said Lee's office had submitted an application and the American Institute in Taiwan, which represents U.S. interests there, adjudicated it according to U.S. regulations. "Based upon these guidelines they issued a tourist visa to Mr. Lee," he added.
A Chinese Embassy spokesman said Thursday Beijing was strongly opposed to Lee's plans to visit Cornell University, where he studied in the 1960s.
In Beijing, Chinese Deputy Foreign Minister Wang Yi called in Japanese Ambassador to Beijing Koreshige Anami to protest, saying issuing the visa "disrupted and sabotaged relations," the government's Chinese Central Television reported late Friday.
Lee, who retired a year ago, says he needs to go to western Japan for treatment of a serious heart condition. He made his request for a visa more than a week ago in Taipei.
He agreed not to engage in any political activity during his stay, Kono said.
The visas were issued amid rising tensions between China and the United States who have been locked in a dispute over a collision between a U.S. spy plane and a Chinese jet fighter.
Also straining U.S.-China ties is an approaching U.S. decision on Taiwan's annual request for arms, including four destroyers with the missile-hunting Aegis radar system, submarines and an advanced Patriot missile defense system known as PAC-3.
The United States is one of only a few nations that sell Taiwan weapons. Washington is obligated by law, the 1979 Taiwan Relations Act, to sell the island weapons necessary for its defense.
Taiwan analysts said Washington was unlikely to sell Taiwan the politically sensitive Aegis system amid the spy plane rift. Instead, less-sophisticated Kidd-class destroyers might be sold.
Also on the island's shopping list are up to 70 Boeing AH-64D Apache Longbow attack helicopters, Harpoon anti-ship missiles, HARM anti-radiation missiles and eight to 12 Lockheed Martin P-3 maritime search and anti-submarine aircraft.
Zhang Yuanyuan, spokesman for China's embassy in Washington, on Thursday predicted a "devastating impact" on U.S.-China relations if the United States decides to sell any advanced weapons to Taiwan this month, including Kidd-class destroyers.
Asked to elaborate, he said: "Well, let's say destructive impact, very bad impact, devastating impact."
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