The Eredivisie side claimed they were due a 30% sell-on fee but Swansea sources say it was a free transfer and the Dutch club are not due any money.
A FIFA spokesperson said: "We can confirm that we've received a complaint from the club FC Utrecht against the club Swansea City in connection with the transfer of the player Michel Vorm.
"At this stage we cannot make any further comment."
Vorm came on as a 93rd-minute replacement in the third-placed World Cup play-off for the Netherlands in their 3-0 win over hosts Brazil.
The 30-year-old moved to the Liberty Stadium in July 2009 for £1.5million before signing a fresh deal at the club in September 2012 to take him up to the summer of 2016.
However, Spurs secured his signature, and that of Swans team-mate Ben Davies, last month.
Davies signed a five-year contract at White Hart Lane, while Vorm signed a four-year agreement. Iceland midfielder Gylfi Sigurdsson moved to south Wales as part of the deals.
Swansea previously said Vorm's transfer did not break any rules.
"The transfer of Michel Vorm was conducted and concluded correctly under Premier League rules," a Swansea spokesman said.
"It was approved by the Premier League and also FIFA via their TMS (Transfer Matching) system.
"While we have been in contact with Utrecht as a matter of courtesy, we will continue to conduct our business in the best interest of our football club and our supporters, and not based on the views of other clubs.
"Unlike some countries abroad, we do not have third party ownership of players in Britain. The club will not be commenting further on this matter."