Opposition party Pheu Thai, the former governing party ousted by the coup, appeared on course to win the most seats.
The Phalang Pracharat party, which wants junta chief Prayut Chan-O-cha to return as Premier, gained more than 7.3 million votes with 91 per cent tallied, according to the EC - almost half a million more than Pheu Thai.
Mr Prayut's party is on track to cobble together the 126 votes in the lower house it needs for a parliamentary majority, in combination with a 250-seat upper house Senate that is appointed by the junta.
In Bangkok Sudarat Keyuraphan, a Pheu Thai prime ministerial candidate said the party was eyeing a coalition but vowed "we will not join" any supporters of Prayut.
Politicians across the spectrum fear a stalemate has been booked-in by new election rules, written by the junta, which limit the chances of any single party emerging with a comfortable parliamentary majority.
There are still 150 "party list" seats in the lower house up for grabs, where the popular vote will matter more.
Thailand's pro-military party has taken the lead in the country's first general election since the military coup of 2014, according to preliminary results.
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Thailand's election was "rigged" to ensure the military retain their grip on power, former premier Thaksin Shinawatra, a towering behind-the-scenes figure in the politically turbulent kingdom, told AFP on Monday. The Democrats have won only about 3.1 million votes.
Just over 65 percent of the 51 million registered voters cast their ballot, the commission said.
This has been made worse by allegations of irregularities, with reports some polling stations had nearly twice as many votes as registered voters.
But even if Pheu Thai manages to overturn the latest vote count, it will face significant obstacles to forming a new government in the lower house.
Thanathorn Juangroongruangkit said the party was overwhelmed at the support it had received and was open to talks with Pheu Thai to form a government.
"The Election Commission should address this issue because if the people feel they can not trust the results, there will be more problems to come", she said.
This was followed by the military-backed Palang Pracharath party with 97 seats.
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The election pits a royalist junta and its allies against the election-winning machine of billionaire ex-premier Thaksin Shinawatra, who was toppled in a 2006 coup, and an unpredictable wave of millions of first-time voters. "This is making people skeptical of the election results", said Future Forward spokeswoman Pannika Wanich.
While the Election Commission said some results would be ready in the coming hours, exact tallies were not due to be finalised until Friday. Final results from the vote are not expected until later this week.
Election night hoisted a new, youth-focused political party with vigorous anti-junta positions - Future Forward party - onto the Thai political stage.
The vote is taking place under a military-backed constitution, Thailand's 20th.
A Phalang Pracharat source said negotiations were on with Bhumjaithai leader Anutin Charnvirakul, Chartthai Pattana leader Kanchana Silpa-archa, Suthep Thaugsuban of Action Coalition for Thailand and Suwat Liptapanlop of Chartpattana. That potentially gives ex-army chief Prayuth a major advantage if the junta-appointed Senate backs him en bloc. "It will be clearer once the official result is announced", he said.
She said the party's legal team was considering whether to submit complaints to the Election Commission.
"Everyone knows in Thailand, everyone worldwide that observed the election in Thailand, knows that (there) is irregularities", he told Agence France-Presse (AFP) in an interview on Monday in Hong Kong.
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Among those present was Yingluck and Princess Ubolratana, who briefly caused a shockwave ahead of the elections when she was announced as a candidate to lead a Thaksin-linked party.