The vote on Saturday for 23 city and county leaders was also seen as an early indication of the strength of newly-elected Nationalist Party leader Ma Ying-jeou, considered the overwhelming favourite to lead the opposition in the 2008 presidential election.
On Thursday, Ma dramatically raised the stakes in the municipal elections, saying he would step down as Nationalist chief if his party failed to win more than half of the 21 major races.
In municipal elections four years ago, the Nationalists and their allies won 13 out of 23 counties and cities, while Chen's Democratic Progressive Party (DPP) and its allies took 10.
With Chen and Ma at the forefront, the campaign has been marked by Taiwan's usual mudslinging, including widespread allegations of vote-buying and fraud.
Civil servant David Ho, 47, said he was disappointed by the dirty campaign, but that it had not turned him off voting.
"I don't like candidates slinging mud at each other, but we have the right to vote so we have to use it," he said after casting his ballot at the Chuwei Activity Centre in Taipei County. Ho did not say which camp he voted for.
"I don't like candidates slinging mud at each other, but we have the right to vote so we have to use it"
David Ho, a civil servant
The Nationalists appeared to have made considerable headway by drawing attention to a major scandal involving a former Chen adviser, and other alleged instances of ruling camp chicanery.
But Chen countered strongly in the final days of the campaign, saying that the opposition's willingness to deal with Beijing threatens the island's sovereignty.
"The result of these local elections will decide the future of cross-straits relations," Chen said. Taiwan and China split at the end of a civil war in 1949.
Beijing still claims sovereignty over the island and has refused to talk with Chen because it sees him as a strong supporter of Taiwanese independence, opposed to the Nationalist platform of eventual unification.
Both the DPP and the Nationalists hope to win more than half of Saturday's races to provide momentum towards the 2008 presidential election.
A DPP defeat would raise friction among contenders to succeed Chen, some analysts say.
The constitution bars Chen from running for a third term, and the DPP is unlikely to choose a candidate until 2007.
"The danger is that a defeat will encourage internal struggle in the run-up to the 2008 presidential elections," said Andrew Yang, a senior analyst at the Chinese Centre for Advanced Policy Studies in Taipei.
Premier Frank Hsieh and DPP Chairman Su Tseng-chang are both potential frontrunners for the presidency, but a poor DPP performance on Saturday could damage their chances.