Embattled Prime Minister Yingluck Shinawatra was among the early voters, casting her ballot in front of the media at a polling station at the Klong Lamchiak School near her house here. TV channels said protesters were not present there.
There were no reports of major violence during the polls that ended this afternoon and was relatively peaceful.
The counting began immediately after the voting ended. After the counting at each station is completed, the results would be sent to the Election Commission (EC) and the outcome will not be announced until after the EC has re-organized elections for advance voting and for blocked polling stations.
Officials said anti-government protesters disrupted the voting at 127 out of 375 constituencies nationwide. The polling was cancelled in most areas of the southern region and in many constituencies in Bangkok.
EC cancelled the poll in 9 of 14 provinces in the South, a stronghold of opposition Democrat Party. The provinces of Songkhla, Trang, Phatthalung, Phuket, Surat Thani, Ranong, Krabi, Chumphon and Phangnga had no voting at all.
All polling stations functioned in the northern and northeastern regions - strongholds of the ruling Pheau Thai party of Yingluck - and 122 out of 127 polling stations opened in the central and eastern provinces, officials said.
In Bangkok, a rally by protesters forced closure of most of the polling stations in Ratchathewi, Din Daeng and Lak Si - the scene of violent clashes between pro-and anti-government protesters yesterday which left at least seven people injured.
Two journalists - a Thai reporter and an American photojournalist - were among the injured.
More than 93,000 polling stations were set up across the country and around 120,000 police personnel deployed. Army deployed 5,000 soldiers in the capital to prevent violence. Over 47 million voters wre eligible to cast their vote today.
The EC will set up a new election date for the areas unable to open today. It could be one week after the new advance voting day scheduled for February 23.
India had advised its citizens to take precautions for their safety, warning that "higher levels of protests are likely, which could lead to violent incidents/disruptions".
Protesters have been holding rallies across Bangkok and have blocked major intersections for the past two months calling for Yingluck's government to quit, an unelected people's Council to be formed and the polls to be scrapped.
The protesters accuse Yingluck of acting as a proxy for her fugitive brother, former premier Thaksin Shinawatra who was ousted in a coup in 2006. He lives in self-imposed exile in Dubai to escape a jail term on a corruption conviction.
However, Premier Yingluck went ahead with the election.
Voting in Phang Nga province in the south was cancelled because ballot papers and boxes could not be delivered to polling units, provincial election committee chairman Peera Phetpanich announced. The province was also unable to recruit enough officials to man all polling stations.
Anti-election protesters in the South have been blocking the delivery of voting ballots at post offices in the region.
The EC had earlier said voting could not be held at 45 constituencies in nine provinces due to anti-government protests. The elite-backed Democrat Party, which has not won an elected majority in two decades, is boycotting the polls.
In the south, protesters stopped post offices from distributing ballot papers and boxes to polling stations in 42 constituencies, said EC secretary general Puchong Nutrawong.
Eight people were injured, two seriously, in three violent incidents hours before voting, local media said.
Advance voting on January 26 was marred by blockades by opposition protesters who stopped hundreds of thousands of people from casting ballots.
The outcome of the poll is expected to be inconclusive as protesters blocked candidate registration in some districts last month hence parliament will not have enough members to convene. Speculation is rife that the army might intervene if the election leads to political limbo.
At least 10 people have been killed and hundreds injured in clashes since the opposition rallies began last year.
The recent violence is the worst political bloodshed in Thailand since 2010 when protests by pro-Thaksin "Red Shirts" left more than 90 dead and nearly 1,900 injured in clashes and a military crackdown.