The chaos was the latest blow to prime minister Yingluck Shinawatra's embattled government, which called the February 2 vote in a failed bid to ease months of street protests.
The outcome of yesterday's balloting is seen as a harbinger for the main poll, which the election commission and protesters demanding that Ms Yingluck be ousted want postponed.
Disruption was expected at 50 polling sites in Bangkok and opposition strongholds in southern Thailand, but voting was likely to have been unhindered in the majority of the country.
About 49 million of Thailand's 64 million people are eligible to cast ballots, and 2.16 million of them applied for advance voting.
Protesters waving the Thai flag blocked electoral officials and ballot boxes from getting inside voting stations, and several were closed as a result.
Police took no action to disperse the crowds, following long-standing orders from Ms Yingluck to avert violence for fear of triggering a military coup.
The protesters, led by Suthep Thaugsuban, are pushing for Ms Yingluck's government to be replaced by a non-elected 'people's council' that would implement anti-corruption reforms before a new vote can take place.