Taiwan ordered the Harpoon missiles in 2008 as part of a USD 6.5 billion arms purchase which sparked strong protests from Beijing.
The island already has Harpoons installed on its frigates and F-16 fighter jets.
The first batch of such missiles for the navy's two Dutch-built submarines has been shipped to Taiwan, the state Central News Agency said, citing a recent report to a closed session of parliament by deputy defence minister Andrew Hsia.
The report said Taiwan spent USD 194 million on the missiles, but did not say how many had been bought and the number delivered.
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The missile has a range of 150 nautical miles (278 kilometres), nearly ten times the range of torpedoes which are currently the subs' major weaponry.
The defence ministry declined to comment on the report.
The US deal also included advanced interceptor Patriot missiles and Apache attack helicopters.
The two sides split in 1949 but China still sees the island as part of its territory awaiting reunification.
Relations have improved markedly since Ma Ying-jeou of Taiwan's China-friendly Kuomintang party came to power in 2008 and was re-elected in January 2012.
But China still threatens to invade Taiwan should the island declare formal independence, prompting it to seek more advanced weapons - largely from the United States.