The Taipei District Public Prosecutor's Office found after a six-month probe that Ma broke laws on the protection of personal information, release of secrets and communications security and surveillance, office spokesman Chang Chieh-chin said.
Ma, 66, a US-educated legal scholar, was credited with substantially improving Taiwan's relations with rival China during his two terms in office from 2008 to 2016. However, his push for ever-closer ties sparked a backlash, especially among young Taiwanese wary of China's intentions toward the island it considers its own territory to be brought under control by force if necessary.
Ma's indictment today comes more than a year after his Nationalist Party was soundly defeated at the polls by the pro-independence Democratic Progressive Party, which has sought to maintain ties with the mainland while asserting the self-governing island's own place in international society.
China responded by cutting off contacts with Taiwan's government in June in protest at new President Tsai Ing-wen's refusal to acknowledge its claim that Taiwan and the Chinese mainland are part of a single Chinese nation.
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China and Taiwan, a former Japanese colony, split amid civil war in 1949.
Wang at the time was speaker of the legislature and Ma's main political rival within the party.
The charges against Ma carry a maximum sentence of three years each.
Ma was barred in June from visiting Hong Kong under a state secrecy law restricting travel by former top officials for three years after leaving office.
Ma spokesperson Hsu Chao-hsin said the former president's denial of the accusations was rejected by prosecutors.