The Kuomintang party (KMT) appears to have lost control of districts across the country, including the mayor's office in the capital, Taipei.
Saturday's polls were widely seen as a referendum on relations with China, informs Report citing BBC News.
KMT supporters had argued for good relations with China, which views Taiwan as a renegade province.
China and Taiwan, a close US ally, have been ruled separately since the end of a civil war in 1949.