Chris Eaton, a former head of security with FIFA, told Channel 4 on Monday night the organisation were looking into a specific incident in the clash between Nigeria and Greece.
However, a FIFA spokesperson said in a statement: "We are not conducting any match fixing investigation for 2010 FIFA World Cup matches.
"Ralf Mutschke is the head of FIFA's new security division. The fight against match fixing is only one of their duties, in addition to stadium security and general event security for all FIFA events including the FIFA World Cup.
"In relation to match fixing, investigations can be launched by the security division in case there is a suspicion a match or a competition could be fixed.
"Any such issues are then reported to the FIFA Disciplinary Committee (in order to sanction members of the football family) as well as to the disciplinary bodies of national Football Associations and/or to law enforcement organisations."
Eaton alleged his former employers were still investigating suspicious activity at the game.
He said: "It's certainly an interesting circumstance and we know a lot about it.
"It's another manifestation and potentially a manifestation of an attempted fraud that could be perhaps replicated in the future so we have to be cautious about it."
While dismissing the claim, FIFA's spokesperson added they are closely monitoring and assisting on-going investigations at member associations' level.