European teams launched the "OneLove" initiative in response to the treatment of LGBTQ communities in Qatar, where homosexuality is illegal.
FIFA though has requested that all captains wear a different armband on each match day, promoting social messages such as "Football unites the world" and "Share the meal" in a United Nations-backed campaign.
"Each round of matches will be associated with its own dedicated campaign designed to maximise reach and impact," FIFA said in a statement.
The move puts football's world governing body on a potential collision course with teams such as Germany, whose captain Manuel Neuer said he would still wear a "OneLove" armband to promote diversity and inclusion.
"Other European nations are wearing (the armband) and it is good we are doing it together," Neuer said on Saturday.
Denmark's Christian Eriksen said his country's captain Simon Kjaer would be wearing the rainbow armband too, regardless of any disciplinary action taken by FIFA.
"We as a country are wearing it, our captain will be wearing the OneLove armband," Eriksen said. "What the consequences will be I don't know, but we'll see."
England's Football Association are also believed to be ready to support the "OneLove" campaign regardless and are understood to be seeking clarity on whether the rainbow armband and the FIFA ones can be worn together.
Contacted by AFP, FIFA did not respond.
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