Thailand's ousted former prime minister, Thaksin Shinawatra, said on Monday that the ruling military junta "manipulated" the results of an election after a party of his loyalists did worse than expected.

Partial results of Sunday's election, the first since a military coup in 2014, showed an unexpected lead in the popular vote for a pro-military party that wants to keep junta leader Prayuth Chan-ocha as prime minister.

"I knew that the junta running Thailand wanted to stay in power, but I cannot believe how far it has gone to manipulate the general election on Sunday," Thaksin wrote in an opinion piece in the New York Times.

Two major political parties also raised doubts about the accuracy of the election results that could see the country's junta chief remain in power.

One party said it was considering a legal challenge over what it said were poll irregularities, and the number of signatures on an online petition to impeach the Election Commission leapt by more than 300,000 over a few hours on Monday to more than half a million.

Sudarat Keyuraphan, the Pheu Thai Party's candidate for prime minister, says irregularities in the election are affecting 'the nation's credibility and people's trust.' (Jewel Samad/AFP/Getty Images)

"There are irregularities in this election that we're not comfortable with. These affect the nation's credibility and people's trust," said Sudarat Keyuraphan, candidate for prime minister of the Pheu Thai Party.

"We've voiced our concerns before for vote-buying, abuse of power, and cheating. All three have manifested. We will fight back through legal means," she told a news conference.

Uttama Savanayana leads the pro-military Palang Pracharat party. The party says it will try to form a government. (Soe Zeya Tun/Reuters)

She said her party, which is linked to the military's nemesis, the self-exiled former leader, would join forces with other anti-junta parties to form a government.

"We have nothing to hide," the commission's deputy secretary-general, Nat Laosisawakul, told a news conference.

Official results delayed until May

The opposition Pheu Thai party won 138 seats in the House of Representatives and its pro-army rival took 96 seats, but the winners of 150 of the lower house seats are still unclear, according to the Election Commission.

The overall winner of the election may not emerge for weeks because the Election Commission has said it will announce the official results of the final 150 seats in the 500-seat parliament on May 9.

The initial results from 350 constituency seats contested were posted on the commission's website on Monday.

'Cheating' trends on Twitter

Despite taking the largest share of parliamentary seats, according to the partial release of results, it appeared that Pheu Thai had fallen far short of expectations, a surprise for many given that Thaksin-allied parties have won every election since 2001.

The strong showing by the pro-junta Palang Pracharat Party stunned voters who had hoped the poll would loosen the grip that traditional elites and the military hold on power in a country that has one of the highest measures of inequality in the world.

Amid mounting confusion over the results of the poll, Palang Pracharat's spokesperson told reporters his party was aiming to muster 251 of the lower house's seats to form a government.

Skewed poll for the military?

Many Thais took to social media to voice their suspicions about the results of an election that critics had said was systematically skewed in favour of the military from the outset.

Thai-language hashtags that translated as "Election Commission screw-up" and "cheating the election" were trending on Twitter in Thailand.

Many tweets referred to inconsistencies between the numbers for voter turnout and ballots cast in some parliamentary constituencies. Some questioned the overall turnout of less than 70 percent, which was much lower than expected.

Future Forward, a new party that appears to have made a spectacular election debut thanks to its appeal to young voters, also questioned the poll numbers.

"There are obviously some irregularities with the numbers because they don't add up. This is making people skeptical of the election results," said party spokesperson Pannika Wanich.

"The Election Commission should address this issue because if the people feel they cannot trust the results, there will be more problems to come," she said.

A change.org petition launched a week ago to impeach the Election Commission had garnered over 511,000 signatures by mid-afternoon on Monday, up from around 200,000 at the start of the day.

Pro-junta party ahead in popular vote

With all but 6 per cent of votes counted, the commission reported that the pro-junta Palang Pracharat was leading with 7.69 million votes. Pheu Thai trailed with 7.23 million votes.

The popular vote numbers did not reflect parliamentary constituency seats won. Pheu Thai could still take the lion's share of these, which are decided on a first-past-the-post basis, because of its popularity in the north and northeast of the country.

The remaining 150 "party list" seats in the lower house will be allocated under a complex proportional representation formula.

However, Prayuth looked in a good position to remain in office thanks to a new, junta-devised electoral system.

The lower house and the upper house Senate, whose 250 members are appointed by the junta, will together select the next prime minister.

Thailand has been racked for the past 15 years by street protests by both opponents and supporters of Thaksin. The populist former telecoms billionaire was thrown out by the army in 2006 and a government led by his sister was ousted in 2014.