The 40 seats contested on Sunday, mostly in southern strongholds of the Democrat Party which led two other opposition parties to boycott April 2 general elections, will still leave some parliamentary seats empty, meaning no quick end to a constitutional crisis that has forced Thaksin Shinawatra, the prime minister, to cede day-to-day power.
Fear and fatigue loomed large in the Malay-speaking south where a two-year separatist insurgency has killed more than 1,100 people, despite declarations from the Buddhist-dominated government in Bangkok that it is winning against the separatists.
On Friday, Chidchai Vanasatidya, the acting prime minister, had said that there would be no repeat of gun and bomb attacks during senate elections on April 19 "because we have taken all preventive measures".
But early on Sunday before voting began, unknown attackers riding on a motorcycle killed one man and wounded a woman near a polling station in the province of Narathiwat.
On Saturday night, fighters blew up a bus shelter in the province of Yala and clashed with policemen and soldiers. A policeman was badly wounded in the head.
Last week five people were killed and 30 wounded in the region comprising the three Muslim-dominated provinces of Narathiwat, Yala and Pattani.
Among the dead were three election officials killed when their truck carrying ballot boxes was blown up.
The government stepped up security after intelligence reports suggested there would be more attacks on Sunday, and double or triple the number of police and troops have been deployed at 466 polling stations in Narathiwat alone.
Acting PM Vanasatidya: We have
taken all preventive measures
Police on trucks and soldiers in armoured vehicles and on motorcycles patrolled remote highways and areas around polling stations in the region.
Some election volunteers feared the heavy security would only draw attacks from fighters targeting police and soldiers.
Ning, a village chief in Narathiwat, said: "You have a 50-50 chance of surviving a militant attack when you travel alone, but your risk is greater with an escort from police or troops."
Even if violence does not disrupt voting in the by-elections, a solution to the constitutional deadlock does not seem imminent.
Around half the 40 seats at stake are contested only by Thaksin's Thai Rak Thai (Thais Love Thais) party and a candidate has to get 20% of the eligible vote to win in a region where the government is very unpopular.
Unless all its seats are filled, parliament cannot convene, no new prime minister can be elected to replace Thaksin and no new government can be formed.
Election officials are expecting a low turnout for the country's third poll in a month.
Padoongyot Duangmala, chairman of the election committee in Pattani province, said: "To be honest, people are tired of elections, both organisers and voters."