Worawi Makudi retained control of the Football Association of Thailand (FAT) after a comfortable win in an election on Thursday.
Worawi defeated former national team manager Virach Charnpanich 42-28 for another two-year term as FAT president.
But Virach, who also lost to Worawi in the previous election two years ago, complained of foul play.
"The election was unfair and not transparent," said Virach, who may take legal action to suspend the result.
But Worawi, who has been Thailand's football chief since 2008, said the election was conducted in a straightforward manner.
"It should be an example for elections in Thai sports because we had an election commission and an appeals committee to oversee it," said Worawi.
It was the first time that there were such panels to oversee an election in Thailand's sporing circles. But their presence could lead to a legal struggle.
Virach claimed that the appeals committee might have sided with Worawi.
Under an agreement, Virach picked three of five members of the election commission and Worawi two, while Worawi selected two of three members of the appeals panel and Virach one.
Virach argued that the election commission had disqualified six clubs but the appeals committee reversed the decision just before yesterday's election.
The six voters were believed to be Worawi's supporters including Korkaew Pikulthong who represented Phangnga FC, Muang Thong United manager Kan Chanrat who represented Nonthaburi FC and Thanya Popaichit who represented Trang FC.
Virach said the six had nothing to do with the clubs they represented.
Yesterday's result must be endorsed by the election commission but reports claimed it will not approve it. The commission is expected to hold a press conference today.
Virach and his backers also had themselves to blame for the defeat.
They had campaigned fiercely against Worawi's push for changes to the association's regulations to be in line with Fifa statutes but he surprisingly made a U-turn and accepted Worawi's proposal a few weeks ago claiming that they did not want the country to be punished by Fifa.
The main point of the changes was a reduction in the number of eligible voters from about 180 to 72.
It was believed that a large number of Virach's supporters were clubs in the lower leagues who became ineligible to vote under the new rules.
Worawi, meanwhile, enjoyed support from several clubs in the top flight including SCG Muang Thong United, BEC Tero Sasana and Bangkok Glass.
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