The Harpoon missiles were launched from Hai Hu (Sea Tiger), a Dutch-built conventional submarine, during a drill last week, the Liberty Times and the United Daily News said, citing unnamed naval sources.
Taiwanese navy started taking delivery of the missiles last year to arm two submarines.
The missiles, which have a range of 150 nautical miles (278 kilometres), would boost the attack capabilities of the two submarines previously only armed with torpedoes with a limited range, the naval sources were quoted as saying.
Taiwan, which already has Harpoons installed on frigates and F-16 fighter jets, ordered the submarine-launched missiles in 2008 as part of a USD 6.5 billion arms sale that sparked strong protests from Beijing.
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The deal also included advanced interceptor Patriot missiles and Apache attack helicopters.
Ties between Taipei and Beijing have improved markedly since Ma Ying-jeou of the China-friendly Kuomintang party came to power in 2008 promising to boost trade links and allow more Chinese tourists to visit the island. Ma was re-elected in 2012.
But Beijing still sees the island as part of its territory awaiting reunification, by force if necessary, even though Taiwan has governed itself since 1949 at the end of a civil war.