(Refiles to correct gender of Pheu Thai party representative, paragraphs 8-9)
* Pro-military party leads popular vote count
* New election system favours pro-military parties - critics
* Thaksin-backed party may have most parliament seats
* Junta chief's future as PM unclear
By Chayut Setboonsarng and Patpicha Tanakasempipat
BANGKOK, March 25 (Reuters) - A party linked to Thailand's military led the popular vote after most ballots had been counted from Sunday's general election, the country's first since a 2014 coup, giving it a surprise advantage over anti-junta parties hoping to make a comeback.
Unofficial results will be announced on Monday afternoon, so it is still not certain that the Palang Pracharat party backing junta chief Prayuth Chan-ocha will have enough lower house of parliament seats for him to stay on as prime minister.
Pheu Thai, a party linked to the self-exiled former premier Thaksin Shinawatra whose loyalists have won every election since 2001, fell short of expectations that it would outdistance the military's proxy party. However, it still looked likely to have the largest share of parliament seats.
The strong showing by the pro-junta party dismayed voters who had hoped the poll would loosen the grip that traditional elites and the military have long held on power in a country that has one of the highest measures of inequality in the world.
Many took to social media to voice their suspicions about the results of an election which critics had said was 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 at numbers one and three on Twitter in Thailand.
Many tweets referred to inconsistencies between the numbers for voter turnout and ballots cast in some parliamentary constituencies, and some questioned the overall turnout of less than 70 percent, which was much lower than expected.
"There is suspicion about extra ballots where the number of ballots was higher than the number of voters in some districts," said Pheu Thai party spokeswoman Ladawan Wongsriwong. "There is also suspicion about reports of vote-buying."
She said the party's legal team was considering whether to submit complaints to the Election Commission.
The Election Commission had planned to announce the unofficial results for the 500-seat lower House of Representatives on Sunday evening but said its announcement had been delayed until Monday, without giving a reason.
With 94 percent of overall votes counted, the commission reported that the pro-junta Palang Pracharat was leading with 7.69 million votes. The Thaksin-linked Pheu Thai Party trailed with 7.23 million votes.
The numbers released were for the popular vote, but these 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 concentrated popularity in the north and northeast of the country.
Based on a Reuters tally of partial results of the 350 constituency seats contested on Sunday, Pheu Thai was on track to win at least 129 and Palang Pracharat at least 102.
Another 150 "party 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.
The means Prayuth's party and allies have to win only 126 seats in the lower house, while Pheu Thai and its potential "democratic front" partners would need 376.
The royal family, which wields great influence and commands the devotion of millions of Thais, played a part in the election though how far this determined the outcome was unclear.
On the eve of the vote, King Maha Vajiralongkorn made an unexpected and cryptic statement, urging voters to put "good people" in power and to prevent "bad people from ... creating chaos".
Although the king did not refer to any of the sides in the election race, there was speculation on social media that it was a coded reference to country's main political factions - broadly the middle class and urban establishment, who identify with the monarchy and the military, and their pro-Thaksin opponents.
King Vajiralongkorn also weighed in last month after a startling turn of events when a pro-Thaksin party nominated Princess Ubolratana, his sister, as its prime ministerial candidate.
Within hours, the king issued a statement saying her candidacy was "inappropriate" and she was disqualified.
The connection between the princess and Thaksin persisted in voters' minds, particularly after they were seen hugging on Friday at the wedding of his daughter in Hong Kong.
"We had a lot of dramas in the last hours before the election," said Thitinan Pongsudhirak, a political analyst at Chulalongkorn University told Reuters. "Thaksin overplayed with a royal involvement and that was countered by his opponent."
Thailand has been racked for the past 15 years by street protests both by Thaksin opponents and his supporters. The populist former telecoms billionaire was thrown out by the army in 2006 and a government led by his sister was ousted in 2014.
(Additional reporting by Panu Wongcha-um, Panarat Thepgumpanat, Kay Johnson and Aye Min Thant Writing by John Chalmers; Editing by Michael Perry)
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