The Brighton and Hove Albion defender has reportedly gone for a scan and the results were still being awaited, as the team left Essentuki for Kaliningrad on Thursday afternoon.
If Balogun is unable to take his place against Croats, Gernot Rohr will likely opt for Kenneth Omeruo.
Injury denied Balogun a spot in Nigeria’s 2014 World Cup squad, after the 29-year-old broke his foot in March of that year.
Ever since his return, he has become first choice in central defence, along with William Troost-Ekong.
Nigeria take Croatia at 8pm Nigerian time on Saturday.