Interpol boss Juergen Stock said he was suspending the deal set up in May 2011 to create a 10-year "Integrity in Sport" programme.
"In light of the current context surrounding FIFA, while Interpol is still committed to developing our Integrity in Sport programme, I have decided to suspend the agreement," said Stock in a statement.
"All external partners, whether public or private, must share the fundamental values and principles of the organisation, as well as those of the wider law enforcement community," added Stock.
The scandal has also cast doubt on the fairness of the bidding process for the 2018 and 2022 World Cups to be staged in Russia and Qatar respectively.
Interpol noted that the agreement with FIFA included a clause stating that "the funding party declares ... That its activities are compatible with the principles, aims and activities of Interpol.