World football's governing body is gathering information after City alleged midfielder Seko Fofana, 20, was targeted during an Under-21 match.
Meanwhile, Fifa has also asked the Italian Football Federation (FIGC) to investigate comments made by the favourite to become its next president.
Carlo Tavecchio reportedly made racist remarks about African players.
A Fifa spokesman says they were aware of the alleged incident in Croatia, which saw City coach Patrick Vieira take his side off the field.
He added: "We are in contact with the relevant member associations to enquire and monitor the situation. We will be in a position to further evaluate the matter, once we gather all the relevant information."
The Croatian Football Federation has already said it will investigate City's claim.
With regards to Tavecchio, a Fifa spokesman added: "Media reports concerning alleged racist comments by one of the presidential candidates for the Italian FA have alerted Fifa's Task Force against racism and discrimination and its chairman Jeffrey Webb.
"As such, Fifa has written a letter to the Italian FA asking it to take the appropriate steps to investigate and decide on this matter and report to Fifa."
Writing on Twitter on Monday, Jeffrey Webb said "the football community is appalled" by Tavecchio's alleged comments, adding: "We urge all football officials to speak and act responsibly, adhering to the principle of respect that every human merits."
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