Beijing reviles Lee, an outspoken critic of China, for trying to break Taiwan out of diplomatic isolation during his 12 years in power, which ended in May 2000. Beijing has warned Japan against allowing Lee to visit.
Lee applied for the visa in order to receive medial treatment from a Japanese doctor for his heart condition.
Lee, 78, underwent an operation in Taipei last November to clear a clogged artery which was attended by the same doctor.
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