Interpol has suspended its 10-year, €20 million partnership with FIFA while world football's governing body remains implicated in bribery allegations.
The international police liaison group has said it will "freeze the use of financial contributions from FIFA" that go towards the fight against match-fixing.
Interpol secretary general Juergen Stock said in a statement that the decision had been taken "in light of the current context surrounding FIFA."
"All external partners, whether public or private, must share the fundamental values and principles of the organisation," the statement said.
Later on Friday, FIFA issued a statement in response to the Interpol announcement.
It read: "We are disappointed to learn of the decision by Interpol to suspend cooperation in the fight against match-fixing in football.
"The success and importance of this programme cannot be understated. Our cooperation over the past four years has been a key part of addressing the trans-national problem of match-fixing.
"This successful programme is unrelated to the current issues surrounding FIFA, and we believe that this unilateral decision will negatively impact the fight against criminal activity, a goal of which no supporter of the sport can be in favour.
"FIFA remains committed to this important and successful collaboration and will work for its resumption at the earliest opportunity. We are currently reaching out to Interpol to further discuss this matter."
Last week, Interpol issued a global alert for two former FIFA officials and four marketing executives who face charges, including racketeering and corruption, in the United States.
The six are among 14 football and marketing officials indicted by the U.S. Department of Justice in its widening corruption 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, linked to $10 million payments that were channelled through FIFA as apparent bribes to vote for South Africa as the 2010 World Cup host.
Warner has been released 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 programme to tackle match-fixing operated from an Interpol base in Singapore.
The timing of the deal signed at FIFA headquarters in Zurich -- three weeks before a presidential election -- was criticised as being a campaigning tool used by president Sepp Blatter.
The agreement includes a clause that the governing body must be "compatible with the principles, aims and activities of Interpol," the police organisation said on Friday.
Blatter has said he will step down as president as a result of the investigations into corruption.