Worawi, a member of the FIFA executive committee, polled 42 votes to Virach's 28 during the election, which was delayed due to the implementation of controversial reforms.
One club was disqualified from the election while there was another 'no vote'.
Three members of the commission were not convinced with the eligibility of all the voters and felt that the election was not clean, local media reported on Saturday.
"As someone who has conducted elections, both nationally and locally, for four years, I found it difficult to approve the result yesterday," Chanin Kaenhirun, a member of the commission, was quoted as saying by Thailand's The Nation newspaper.
"We had a case in which people were taking the place of the clubs' representatives."
Virach had appointed three members of the commission while Worawi chose three for the five-member appeal panel as part of a pre-election understanding.
"On the eve of the poll, we held a hearing for those clubs in dispute over voting rights and made a ruling on each case. Our decision was based on FIFA criteria," Chanin added.
"However, just a few hours before the election, the 'new' appeal panel decided to reverse our ruling without reasonable explanation."
Worawi, president of FAT since 2007, had called the election 'transparent' while Virach, who also lost out to the 62-year-old in the vote two years ago, complained of foul play.
Chanin said the Sports Authority of Thailand will take the final decision on the matter.