The Nobel Peace Centre (NPC) and Fifa have been partners in the "Handshake for Peace" initiative between team captains and officials since 2012.
But the centre, an offshoot of the Nobel Committee which awards the Nobel Peace Prize said on Monday that "the board of directors asked management to end cooperation with Fifa as soon as circumstances permit".
Fifa, which has been engulfed by an unprecedented corruption scandal, responded: "We are disappointed to have learned from the media about the Nobel Peace Center's intent to terminate the cooperation with FIFA on the Handshake for Peace initiative.
"Fifa is reluctant to accept this unilateral approach on what is a joint initiative between the football community and the Nobel Peace Centre. "This action does not embody the spirit of fair play especially as it
obstructs the promotion of the key values of peace-building and anti-discrimination."
FIFA said that Bente Erichsen, the centre's chief executive officer, "stressed in a telephone conversation with FIFA president (Sepp) Blatter this morning that the NPC continued to believe in this initiative and hoped it
would live on in football with Fifa".
The Nobel statement on Monday did not explicitly refer to the accusations of corruption at FIFA that have delivered a body blow to the organisation's prestige.
Fifa has been increasingly isolated since May, when a US investigation into the corruption allegations brought charges against 14 people.
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The scandal spectacularly brought down Fifa boss Blatter and 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.
On Friday, Interpol pulled out of a 20 million euro ($23 million) deal with the organisation to promote integrity in sport. And several sponsors -- including Coca-Cola, Adidas, Visa, McDonald's and
Hyundai -- have welcomed an announcement by Blatter that he would resign.