FIFA has claimed that the Nobel Peace Center has hampered "peace-building and anti-discrimination" by withdrawing from the Handshake for Peace initiative.
The initiative was intended to promote a message of peace with handshakes between team captains and officials before matches, but the Oslo-based body has ended this arrangement without specifying a reason.
It is thought that the decision is linked to the corruption scandal that has engulfed FIFA and has seen 14 of its more senior former officials and business executives indicted on corruption charges.
A FIFA statement said: "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 Center.
"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."
The world football governing body added that the Handshake for Peace would remain protocol at the Under-20 World Cup in New Zealand and the Women's World Cup in Canada.