The Local Administration Department (LAD) has reportedly said the Football Association of Thailand's (FAT) revised charter may contradict Thai laws.
In a reply to the Sports Authority of Thailand (SAT)'s letter seeking the LAD's advice, the department said parts of the FAT's revised regulations could be in violation of the Civil and Commercial Code, and even the Constitution.
The LAD's letter to the SAT was published on www.thailandsusu.com and picked up by several media websites.
Acting FAT president Worawi Makudi has tried to change the organisation's regulations to comply with Fifa statutes.
He and the world football's governing body have said the FAT must adopt its revised regulations to be in line with Fifa statutes before an election for FAT president can be held.
Failure to do so could result in Thailand facing suspension, according to Fifa and Worawi, who is also a Fifa executive member.
His opponents want an earlier election date, saying the FAT should first organise the election and allow the new administration to push for changes to its charter.
At the centre of the controversy is the number of eligible voters. Worawi says it must be 72 as recommended by Fifa but his opponents want it to remain at about 180.
The FAT has about 180 members and the LAD said in the letter that all members, and not just 72, should have the right to vote to elect the FAT president.
The revised regulations state that "a court of law is a court of the state which listens to the public and solves legal conflict" may contradict the Constitution which says there are three courts: the lower court, the appeals court and the supreme court.
All associations in Thailand are under the LAD which is an agency under the Interior Ministry.
Worawi has scheduled Aug 9 for its members to vote on the FAT's revised regulations.
Worawi's term ended on June 16 and according to the FAT's current rules, an election for a successor must be held within 30 days of the incumbent's term expiring.
Worawi will be challenged by former national team manager Virach Charnpanich who is backed by Thai Premier League powerhouses Chonburi FC and Buriram United.
Acting FAT secretary-general Ong-arj Kosinkha declined comment on the LAD's remarks saying he had not yet received the letter.