"The people have cast a vote of no confidence in the Ma government. They think his government's economic policies are failing, the nation's dignity is hurt and high-ranking officials are indifferent to public opinion," she said.
The elections saw contests in 17 counties and cities and involved only 38 per cent of the electorate.
Polling followed 174 arrests covering more than 2,400 cases of vote buying and election-related violence, the Taiwan justice ministry said.
Ma's Nationalist Party (KMT) won in 12 counties and cities in the poll but with severely reduced majorities in several locations.
An independent candidate was the winner in one county.
The DPP's rule of Taiwan from 2000 to 2008 brought serious tensions with China, which claims the island as its territory despite having had no control there since the end of the Chinese civil war in 1949.
The relationship has improved dramatically since Ma became president, but his push for better ties has prompted suspicion among a sizable part of the island's electorate.
Ma's government has also come under fire for its handling of August's devastating Typhoon Morakot, and for a decision to import more US beef products despite health concerns.
Ma, whose popularity fell to an all-time low of 16 per cent during the typhoon crisis, has defended his policy of boosting ties with China as leading to future prosperity for the island.