As counting continued on Sunday evening, the Electoral Commission of Thailand projected at 10pm local time (2am AEDT) that Prayut's Palang Pracharat party was forecast to win 139 seats in the 500 member lower house. Pheu Thai looked to have captured about 150 seats, with 50 per cent of the vote counted.

The results put Prayut – who had been serving as prime minister under the military regime – in the box seat to retain power under Thailand's new electoral system, which heavily favours the current regime, and all but guarantees Prayut will remain the country's political leader.

Thailand's election was billed as a clash between democrats and supporters of the military regime. The result has defied public opinion polls conducted in the lead up to the vote, as well as exit polls on the day which suggested Pheu Thai and other opposition parties were on track to easily win a majority of seats.

Junta leader Prayut took power in a coup in 2014. He will likely be joined in an alliance with the pro-marijuana, pro-Grab Bhumjaithai Party, which looked set to win 55 seats, and the royalist Democrats, who were smashed in their Bangkok stronghold on election day and looked like claiming just 35 seats.

Pheu Thai, who are aligned with deposed former prime ministers Thaksin Shinawatra and his sister Yingluck Shinawatra, performed well in their north-eastern stronghold but will ultimately be disappointed with this result.

This election is the first since 2001 in which a Shinawatra-aligned party has not claimed a big majority in parliament.

The Future Forward Party, a new group led by charismatic 40-year-old billionaire Thanathorn Juangroongruangkit, who opposed the military regime, was on track to claim a strong 85 seats in its first showing.

Suggestions of polling irregularities, including vote buying and of senior military officials monitoring how soldiers voted at polling places, circulated on social media though the day on Sunday.

In addition a large number of votes – more than 1.7 million – were ruled invalid by the Electoral Commission.

This statistic could raise further questions about the poll after an election campaign that saw a major ally of Pheu Thai, the Thai Raksa Chart party, completely disqualified after Princess Ubolratana Mahidol was announced as its candidate – and then rapidly disqualified by her brother, King Maha Vajiralongkorn.

At least some of those invalid votes may have been intended for Thai Raksa Chart.

But it was Palang Pracharat's performance – which was better than expected in Bangkok, central Thailand, and in Thailand's populous north – that was the biggest surprise on polling day.

The Democrats, who had set a target of winning 100 seats and who are led by former prime minister Abhisit Vejjajiva, were devastated and their leader quit.

The results meant that Pheu Thai, Future Forward and other opposition parties will struggle to claim the 251 seats needed for a majority in the lower house.

More consequentially, under the country's complicated new constitution the prime minister is chosen by a combined majority of 376 MPs across the 500 member lower house and the 250 member senate, which has been hand-picked by the military junta.

In effect, Prayut only needed to win the support of 126 MPs in the lower house to be chosen as prime minister. Pre-election polls had tipped his Palang Pracharat could win as few as 60 seats – less than half the number they eventually appeared set to win.

The target of 251 lower house seats is now a consolation prize for the opposition parties as it will allow them to hold a majority of seats from opposition, which would allow them to hold Prayut to account. The former general cannot rely on the hand-picked 250 senators to stave off censure or no confidence motion in the parliament.

Voter participation in the poll looked to have reached 67 per cent – down from about 70 per cent in 2011. About 51 million Thais were eligible to vote in the poll, including about 7.1 million Thais for the first time.

Official results from the electoral commission are due no later than May 9.