In an unusually strongly-worded statement, football's governing body added that it was disappointed to hear about the news through the media.
"We are disappointed to have learned from the media about the Nobel Peace Centre's intent to terminate the cooperation with FIFA on the Handshake for Peace initiative," said FIFA in a statement.
"FIFA is reluctant to accept this unilateral approach on what is a joint initiative between the football community and the Nobel Peace Centre (NPC).
"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 NPC announced on Monday that it was ending its link with football's scandal-plagued governing body and did not give a specific reason.
FIFA said NPC executive director Bente Erichsen phoned president Sepp Blatter on Tuesday morning and that she "continued to believe in this initiative and hoped it would live on in football with FIFA".
The Oslo-based NPC was behind the Handshake for Peace Initiative, something that had been enthusiastically promoted by Blatter for three years.
SIMPLE GESTURE
FIFA encouraged pre-match handshakes between team captains and officials as the Handshake for Peace and was also hoping to introduce it at the end of matches.
"The Handshake for Peace initiative combines football’s international reach with the simple gesture of a handshake to promote peace and fair play," said FIFA.
"At FIFA’s tournaments, players and officials use the Handshake for Peace to set a good example in front of both the fans inside the stadium and the wider public watching games on television."
FIFA said the Handshake for Peace would remain protocol at the under-20 World Cup in New Zealand and the women's World Cup in Canada.
The NPC's announcement came three days after Interpol suspended a 20 million euros ($22 million) arrangement with FIFA on fighting match-fixing as allegations of corruption continued to rain down on the ruling body.
The FBI is investigating bribery and corruption involving FIFA officials including scrutiny of how the organisation awarded World Cup hosting rights to Russia in 2018 and Qatar four years later.
Last month nine current or former FIFA officials and five business executives were indicted on corruption charges.
Blatter was re-elected for a fifth term as president in May but announced four days later he would stand down and call a new election.
(Editing by Tony Jimenez)
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