Refusing to recognise the election as legitimate, the opposition boycotted Sunday's polls, which Thaksin called three years early to counter the street campaign.
The result is that nearly 70% of the 399 seats at stake were uncontested and many will be left empty, according to election rules - preventing a new government being formed.
Thaksin's opponents called on voters to tick the "no vote" box on their ballots, a strategy that appeared to work in Bangkok. With half the votes counted in the capital, "no votes" were in the majority, Channel 7 news reported.
The city is usually the first to report results.
But Thaksin's main support comes from the countryside and early returns showed he was getting solid support there - enough to hand him another big parliamentary majority.
Thai media reported turnout was around 70% of the 45 million electorate, compared with 73% in the last election in February, 2005.
Final official results were expected late on Monday.
Thaksin called the election to prove he had majority support against what he called "mobs" accusing him of corruption, cronyism and abuse of power.
He said he would step down if his Thai Rak Thai (Thais Love Thais) party got less than 50% of the vote, which looked unlikely.
Somjai Phagaphasvivat, a political scientist, told Reuters: "The poll will produce a protracted deadlock for months. The final outcome is far from certain."
Thaksin (C) called snap elections
three years ahead of schedule
By 1730 GMT, vote counting was under way in just over half the constituencies. Results were expected to trickle in through the night.
Prasert Suthisonth, the Election Commission spokesman, said: "Before midnight tomorrow, we should be able to get the results of all 400 constituencies."
They were expected to show a huge win for Thaksin as rural Thais – 70% of the country's 63 million people - turned out in force to vote for a prime minister who has given them cheap healthcare and credit during his five years in office.
Pre-election opinion polls showed people were wearying of constant street protests and the disruptions they caused, feared things could only get worse.
Ponganan Limprajikul, a 32-year-old businessman, said: "Most people don't trust elections any more. I think there will be more protests. More people will come out to join the protests and they could become more emotional."