City's Elite Development Squad - who are managed by Patrick Vieira - were led off the pitch in the first half of their match in Novigrad, after midfielder Seko Fofana was allegedly taunted.
The CFF confirmed it is investigating the incident in a statement, despite Rijeka manager Ranko Buketa refuting the claims made by the City teenager.
"Croatian Football Federation is in a process of gathering information regarding the alleged incident and if there are any decisions to be made we'll make it public on our website," the statement read.
"CFF follows a strong "no racism" policy so we take all accusations of racism very seriously.
“Fight against racism (and any sort of discrimination) is one of the key components of our president Davor Suker's programme and that is why we will have a good look into this matter."
Fofana, a France Under-19 international who joined City from FC Lorient in January 2013, received a red card on the stroke of half-time but alleged he was targeted by Rijeka players in the aftermath.
After consultations with the referee, World Cup winner Vieira took the decision to lead his team off the pitch – a decision for which Buketa claimed the former French international had an ulterior motive.
If these claims are true, this is the fourth incident of racist abuse being directed towards City players in the last two years.
Atletico Madrid were fined 10,000 euros after fellow youth player Devante Cole, the son of former Manchester United striker Andy, was abused in March.
CSKA Moscow were ordered to close part of their stadium after monkey chants were directed at midfielder Yaya Toure during a Champions League match in October.
And FC Porto were fined £16,700 after the same chants were directed towards Toure and former striker Mario Balotelli in a game in 2012.