Just days before Sunday's election, Pheu Thai said the houses of party officials and its campaign canvassers in some provinces were searched by military personnel in an act of intimidation. The Thaksin-linked Pheu Thai Party trailed with 7.23 million votes, showed the initial data.
Future Forward, a new party that appeared to have made a spectacular election debut thanks to its appeal to young voters, also questioned the poll numbers.
Pheu Thai secretary-general Phumtham Wechayachai said that the party was seeking collaboration with other pro-democracy parties and would discuss the PM candidate to find the best option for the country.
Despite that head start, analysts had not expected the army-linked Phalang Pracharat party to win the popular vote, given anger at junta rule and the enduring popularity of Thaksin's Pheu Thai.
The elections on Sunday were the first since the coup in 2014 but were held under a new constitution created to weaken the power of the main political parties and entrench military influence through its appointment of the upper house, which will also have a role in choosing the prime minister.
Pheu Thai leader Sudarat Keyuraphan earlier told reporters that the party, which is backed by exiled tycoon Thaksin Shinawatra and has won every election since 2001, was in talks to from a coalition.
Sunday's election was seen as a referendum on the military's five-year rule but was held under new rules written by the junta to ease its transformation into a civilian government.
The partial result did not say how numerous Lower House of Parliament constituencies its results reflected.
Thailand's highly anticipated election results have been delayed as competing parties claim victory and concerns of irregularities and allegations of cheating grow.
The election is the latest chapter in a almost two-decade struggle between conservative forces including the military and the political machine of Thaksin Shinawatra, a tycoon who upended tradition-bound Thailand's politics with a populist political revolution.
Thailand has a total of 51.2 million eligible voters, including some 7.3 million first-time voters nationwide.
It might, however, be possible to roughly calculate the shares of the 150 "party seats" on Friday, when the Election Commission is due to give a breakdown of votes cast.
The electoral body put voter turnout at over 65 percent - a figure critics said was too low and seemed to contradict pre-election polls and the long lines outside of polling stations.
"You cannot say what you want or what you think, you cannot protest because they will take you to the jail", she said. The election is the first since former Prime Minister Yingluck Shinawatra was ousted in 2014. "This is making people sceptical of the election results", said party spokeswoman Pannika Wanich.
Thaksin's aides said he would not answer questions on the royal family, citing the kingdom's lese majeste laws.
In its 2pm press conference today (Mar 25), the Election Commission (EC) announced that although more than 90% of the votes in Sunday's general election had been counted, the wait would continue for the complete interim results.
The commission said full, official results would not be available until May 9. "It's not good for Thailand".
"Everyone knows in Thailand, everyone worldwide that observed the election in Thailand, knows that (there) is irregularities", he told AFP in English.
The military-drafted constitution, Thailand's 20th since absolute monarchy ended in 1932, empowers appointed soldiers and bureaucrats at the expense of elected politicians.
She also urged the 250-member junta-appointed senate to "act in line with the will of the people", a reference to system which allows the upper house to appoint a premier from a minority government. Pheu Thai were also hobbled by the dissolution of Thai Raksa Chart, their sister Thaksin-allied party, which had been a key part of Pheu Thai's strategy to gain a majority in parliament.
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