The clashes broke out as the police tried to disperse protesters who were attempting to ransack a polling booth in the municipality of Takerboust, in the Bouira region, 125 kilometers (80 miles) southeast of the capital, El Watan said, citing residents.
The youths, who have been demanding an inquiry into the running of the commune for the past five years, were seeking to disrupt the vote, some of them told the French-language daily.
Several protesters were arrested and the incident temporarily interrupted voting.
In Haizer, in the same region, residents threatened to boycott the municipal and regional elections and to shut down polling centres, to protest against the military presence in their commune.
Voting was suspended for two hours, but resumed after the intervention of the civil and military authorities, residents said.
Several political parties, including Algeria’s oldest opposition group, the Socialist Forces Front (FFS), claimed that troops voted in their communes.
More than 21 million Algerians are eligible to vote in the election of 1,541 municipal and 48 regional assemblies.
Turnout is considered the only real issue in the election, which President Abdelaziz Bouteflika’s ruling party, the National Liberation Front (FLN), is widely expected to win.
Participation stood at 14.63 percent by 1200 GMT, according to interior minister Dahou Ould Kablia, down from 19 percent at the same time in November 2007 elections.
Polling stations were due to close at 1800 GMT, with the interior ministry expected to announce the results late on Thursday or on Friday morning.