If the preliminary results hold, it will likely add to almost two decades of political instability in Thailand.
Sunday's election - seen as a referendum on the military - was held under new rules written by the junta to ease its transformation into a civilian government.
The overall victor of Sunday's election, the first since a 2014 coup, 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.
A party backed by the military has taken the lead in Thailand's first election since the 2014 coup, indicating that the retired general Prayuth Chan-ocha will stay in power.
Pheu Thai, the party of exiled former Prime Minister Thaksin Shinawatra, said it will try to form a government, even if it loses the popular vote, by building a coalition with other parties.
Third was Future Forward, a party set up only a year ago by billionaire vehicle parts tycoon Thanathorn Juangroongruangkit, with 29 seats.
"People are trapped in this illusion of peace and stability portrayed by the military", he told Al Jazeera.
"Everyone knows in Thailand, everyone global that observed the election in Thailand, knows that (there) are irregularities", he told AFP in English.
But Shinawatra-linked parties have won all elections since 2001, and they are projecting to win 150-200 seats.
"We have the highest vote and following the Thai constitution, whoever has the highest vote will be the one to form government", said Sonthirat Sonjirawong, the secretary general of Phalang Pracharat, which was formed by the junta as a way to hold on to power through the ballot box and secured about 7.9 million votes nationwide.
However, in a late twist, Ittiporn Boonprakong, the commission's chairman, said that the full unofficial results would only be declared this morning, without giving any reason for such a delay.
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The Election Commission has said it will finalise the results by May 9.
Pro-army Palang Pracharatarty spokesperson Kobsak Pootrakool told reporters it has planned to form a government after winning votes in the nation's first election since 2014 coup. Unsettled foreign investors have pulled out in excess of a net $700 million from Thai stock and bond markets this year.
Concerns from the Thai middle-class and business interests kept the pressure on the junta to call elections, although the date was put back several times, as the military sorted out its proxy party support.
As rivals scrambled to seize the momentum and persuade other parties to join forces in a coalition, Thaksin - who had remained tight-lipped in the months running up to the vote - hit out at the junta.
More than 33 million voters out of the 51 million eligible cast their ballots in the election. Critics say the charter gives appointed soldiers and bureaucrats in a planned 250-strong Senate the power to stifle elected politicians in the 500-seat lower house.
The country's young people backed the Future Forward Party, led by Thanathorn Juangroongruangkit - a 40-year old progressive, athletic billionaire, seeking to end military rule - as the hashtag #OldEnoughtoVoteOurselves trended on social media Sunday.
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.
And he mentioned "some vote buying in front of the poll station".
Thailand's powerful King Maha Vajiralongkorn had issued a statement on the eve of the election that said the role of leaders is to stop "bad people" from gaining power and causing chaos. The military may be able to nominate and confirm Prayuth but its highly unlikely that they would be able to govern effectively with a minority government.
Thaksin's sister Yingluck was herself ousted in a 2014 putsch, and is also living in self-exile.