The Bank of China, the mainland's third-largest lender by assets, and Bank of Communications, the fifth-largest, was authorised to invest $40 million and $51 million, respectively, in the branches, the Investment Commission said on Tuesday.
The two banks have operated representative offices on the island for more than a year prior to being allowed to open branches.
Taiwan and China in 2009 signed a package of agreements on better cooperation in banking, insurance and securities, amid improving ties.
China still considers Taiwan part of its territory, even though the island has governed itself since 1949.
But ties have improved markedly since Beijing-friendly Ma Ying-jeou became Taiwan's president in 2008. He was reelected for a second four-year term this month.
Chinese firms had invested around $184 million on the island since it relaxed rules on mainland investment in mid-2009, according to Taiwanese government data.
Chinese investors are currently permitted to buy into nearly 250 categories in Taiwan's manufacturing, service and infrastructure sectors, and the government is planning to further relax rules in March.
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