The FIF claimed via Twitter on Wednesday that striker Bony has sealed his move to the Premier League champions.
"Striker Wilfried Bony has just signed with Manchester City on this Wednesday, January 14, 2015." read a tweet from the federation.
Swansea responded by revealing that the 26-year-old's switch, for a reported fee of £28 million, has not yet gone through.
The Welsh club tweeted: "Wilfried Bony has NOT yet completed his move to @MCFC. Once completed, we will confirm via official channels - not the Ivory Coast FA! #busy."
Bony is currently on international duty preparing for the Africa Cup of Nations in Equatorial Guinea.
The former Vitesse man is reportedly set to join Manuel Pellegrini's side later on Wednesday.
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