FIFA said Wednesday that Makudi would face an investigation by its ethics committee ''should there be any evidence of any potential breach of the Code of Ethics.''
''FIFA is currently seeking clarification with Mr. Makudi on the issue of the FIFA Goal projects in Thailand,'' the governing body said in a statement. ''We cannot speculate at this stage if any of the rules and regulations regarding the awarding of a Goal project have been breached.''
The allegations reported by a Swiss business newspaper relate to funds allocated for the Thai football federation's technical center at Nongiok, near Bangkok.
Makudi is president of the federation, which used $460,000 of FIFA funding in 2004 to build a pitch with artificial turf, according to a project report published on FIFA's website.
The federation received $400,000 in 2007 to build a three-story headquarters providing ''the necessary space for professional leadership,'' FIFA said.
Makudi has previously told Thai media the land was signed over to the national football body.
The 59-year-old official has been a member of FIFA's executive committee for 14 years and is a close ally of Mohamed bin Hammam, who was banned for life by the governing body's ethics panel in July over an alleged election bribery conspiracy.
Makudi could face his own ethics probe if FIFA believes he might have broken article 5 of the code relating to conflicts of interest.
''Private or personal interests include gaining any possible advantage for himself, his family, relatives, friends and acquaintances,'' the code states.
The FIFA Goal project allocates millions of dollars each year to fund football development in FIFA's less developed member nations. It was created by FIFA President Sepp Blatter in 1999, and the committee allocating funds was chaired since then by bin Hammam.
Thailand got the maximum $400,000 grant twice within a four-year spell to develop its national center.
It also used $60,000 of its annual $250,000 grant, which all FIFA members receive, toward the artificial turf pitch project. Blatter officially opened it in September 2009.
Makudi has already been quizzed by FIFA investigators as a witness during the bin Hammam investigation.
He accompanied the Qatari candidate to Trinidad in May when Caribbean officials were allegedly offered $40,000 in cash to back a challenge to Blatter.
Makudi met the FIFA-hired agency of one-time FBI director Louis Freeh, and said he saw no evidence of wrongdoing.
On Thursday, FIFA will hear bin Hammam's appeal against his life ban though he is not expected to attend in Zurich.