The international police liaison group said it will "freeze the use of financial contributions from FIFA" which are used to fight match-fixing.
Interpol secretary general Juergen Stock took the decision "in light of the current context surrounding FIFA."
By distancing itself from FIFA, Interpol added to the toxic image of soccer's governing body.
The Vatican had hours earlier suspended a deal to accept charitable funds from CONMEBOL, the South American soccer confederation which is implicated in the ongoing U.S. federal investigation of widespread corruption.
Interpol's relations with FIFA are closely tied to President Sepp Blatter, who has said he will step down as a result of the corruption investigations.
"All external partners, whether public or private, must share the fundamental values and principles of the organization," Stock said in a statement.
FIFA seemed to be stunned by the move, and said it was "reaching out" to the Lyon, France-based Interpol for talks.
"This successful program is unrelated to the current issues surrounding FIFA and we believe that this unilateral decision will negatively impact the fight against criminal activity," FIFA said in a statement.
Last week, Interpol issued a global alert about two former FIFA officials and four marketing executives who face racketeering conspiracy charges in the United States.
The six are among 14 men indicted by the U.S. Department of Justice in a widening investigation. Four more men have made guilty pleas and further indictments are expected.
An Interpol alert was issued for disgraced former FIFA vice-president Jack Warner, who is linked to $10 million payments channeled through FIFA as apparent bribes to vote for South Africa as the 2010 World Cup host. Warner has been let out on bail in his native Trinidad and Tobago and is to return to court on July 9.
In May 2011, FIFA agreed to fund a 10-year program to tackle match-fixing operated from an Interpol base in Singapore. It was hailed then as the largest private donation ever received by Interpol.
The timing of that deal — three weeks before a presidential election — was criticized as a campaigning tool used by Blatter. The partnership was signed at FIFA headquarters in Zurich by Stock's American predecessor, Ronald Noble.
One year later, Noble was key to recommending Michael Garcia to FIFA when it appointed the former Interpol vice-president as its ethics prosecutor.
The agreement between Interpol and FIFA includes a clause that FIFA must be "compatible with the principles, aims and activities of Interpol," the police body said Friday.
Four years ago, FIFA said the project "will provide cutting-edge training, education and prevention to protect the sport, the players and the fans from fraud and corruption."