FIFA say the case will be passed to the ethics committee if there is any evidence Makudi has breached the code of ethics.
There have been allegations in Thailand that the country's national football training centre was built with money from FIFA's GOAL programme on a plot of land owned by Makudi, and that he owns other plots of land around the centre.
Makudi has previously told Thai media he had signed over the land to the Thai FA.
FIFA said in a statement: "We can confirm that FIFA is currently seeking clarification with Mr Makudi on the issue of the FIFA Goal projects in Thailand. FIFA has sent a letter to Mr Makudi and is following up on this matter.
"Should there be any evidence of any potential breach of the code of ethics, then the matter would be referred to the ethics committee in compliance with article 16 of the code of ethics. However, at the time of writing, no ethics proceedings or ethics investigation has been opened against Mr Makudi.
"We cannot speculate at this stage if any of the rules and regulations regarding the awarding of a Goal project have been breached."
Makudi is a close ally of Mohamed Bin Hammam, who was banned for life in July by FIFA ethics committee for bribery. The Thai accompanied Bin Hammam to the meeting in Trinidad in May where cash gifts were said to have been paid.
Makudi was interviewed by investigators and told them he saw no evidence of cash gifts being made, or heard any talk of it.
Former Football Association chairman Lord Triesman alleged in Parliament that Makudi had demanded the TV rights for a proposed friendly between England and Thailand in return for his 2018 World Cup vote.
Makudi denied that was the case, and an inquiry into the Triesman claims by barrister James Dingemans, commissioned by the FA, did not find any further evidence to support the allegation.
Bin Hammam has appealed against his life ban and FIFA's appeals panel will hear the case in Zurich on Thursday.
Meanwhile, FIFA president Sepp Blatter has described as "pure nonsense" an internet report that he may stand down early and make way for Michel Platini.
The report quoted 'insiders' saying Blatter was considering such a move but he insists that is not the case.
Blatter was re-elected unopposed in May but has promised to step down at the end of his four-year term. Platini, the UEFA president, is seen as his most likely successor.
Blatter said on his Twitter account: "The existence of a reported 'deal' between me and Michel Platini for the FIFA Presidency is pure nonsense.
"The suggestion that I intend to stop my four-year mandate before its end is simply ridiculous."
Blatter had been challenged by Bin Hammam, who pulled out of the race days before the election after being charged with bribery during his presidential campaign.
Makudi insisted he has responded to FIFA's request already and that all was above board.
He told the Daily Telegraph: "FIFA have written to me and I have responded to them already with my legal opinion and it is all finished.
"I believe that I have all the legal papers that show everything was done according to official procedures. We have nothing to worry about."
Asked about the possibility of him facing an investigation, Makudi added: "For what? It is not right that FIFA have not said I have replied to them. I would like them to say more."