Both Kovacic and Gomez were unavailable for the Citizens' 2-0 home win over Everton in the Premier League on Saturday, while Gvardiol watched on as an unused substitute.
All three players were then absent from a 15-minute open training session held on Monday morning ahead of the team's flight to Copenhagen.
Man City have since announced their 21-man travelling squad to Scandinavia and none of Kovacic, Gvardiol or Gomez have been selected.
It is thought that both Kovacic and Gvardiol have picked up minor injuries, while the reason for the absence of Gomez – who has missed City's last two Premier League games against Brentford an Everton – remains unknown.
Kovacic and Gvardiol – two summer signings – have featured regularly in their debut seasons with the Citizens, with both players making 27 appearances in all competitions.
Gomez, meanwhile, has struggled for game time under Guardiola this term, featuring just 10 times in all tournaments, although four of his appearances have been in the Champions League, including two starts.
Guardiola did not provide a fitness update on his squad at a press conference on Monday ahead of the trip to Copenhagen and instead discussed the challenges that his City side could face against the Danish outfit.
The absence of Kovacic, Gvardiol and Gomez has seen City call up two academy prospects in the form of Mahamadou Susoho and Jacob Wright, the latter of whom was on the bench against Everton last time out.
Guardiola also has plenty of senior names at his disposal including
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