Secretary-General Ronald Noble made the comment as Interpol and world football officials wrapped up a two-day meeting in Kuala Lumpur with a pledge to work more closely in combatting the growing scourge of match-fixing.
In a press conference closing the gathering, Noble took aim at Tan Seet Eng, also known as Dan Tan, who has emerged as a central figure in the suspected rigging of nearly 700 games worldwide.
"The fact that there can be an alleged organised crime head operating in a country known to be safe, secure like Singapore, distresses Singaporeans and distresses the world," said Noble.
However, he praised the city-state for tipping off Interpol and Italian authorities on the arrival in Milan on Thursday of an alleged associate of Tan's who is wanted in Italy over match-fixing charges.
Noble did not name the man, who flew to Milan from Singapore, or provide his nationality. Singaporean police denied comment.