The Netherlands international goalkeeper joined Swansea from Utrecht in 2011, and made 89 Premier League appearances for the Liberty Stadium club.
Vorm signed for Tottenham last month and Wilco van Schaik, general manager of Utrecht, claimed last week that his club were owed money on the back of that transfer.
Van Schaik declared that Utrecht were entitled to 30 percent of the sell-on fee for the keeper, as agreed when the 30-year-old left - with Swansea countering that Vorm's sale to Tottenham had been "conducted and concluded correctly".
But on Tuesday Fifa revealed Utrecht had lodged an official complaint against the Premier League side.
"We can confirm that we have received a complaint from the club FC Utrecht against the club Swansea City in connection with the transfer of the player Michel Vorm," a Fifa spokesperson said.