The Germany international celebrated his two goals in Saturday's 2-1 Bundesliga victory over Elversberg with a crown gesture associated with the religious campaign "The King's Return".
Dortmund's Fan and Supporters Department subsequently raised concerns about the network's values, citing investigations by German broadcasters.
Responding to Kicker, the club defended religious freedom while stressing the importance of mutual respect and its shared values.
Dortmund also promised to address supporters' concerns through discussions with Nmecha.
According to Kicker, the Bundesliga outfit have removed social media photographs showing the midfielder using symbols associated with Ballers in God and avoided publishing images of his latest celebrations.
