Claus Thomsen told Reuters it was "responsible management" for the clubs to look at alternatives in case the Champions League turned into a closed shop in a few years' time.
He added that European football had reached a decisive moment where the traditional system based on sporting results was at risk of being replaced.
Organiser UEFA has approved changes to the Champions League for the 2018-21 cycle that critics have said favour the biggest clubs and will increase the financial gap between them and the rest.
Thomsen said teams outside the major countries were right to interpret it as a move towards a Super League.
The decision to use the historical results of clubs as one of the criteria for revenue distribution, plus the creation of a subsidiary partly controlled by the clubs to administer European competitions, were both warning signs, he added.
"The only conclusion you can reach as responsible management in a club the size of Copenhagen, or other big-sized clubs in mid-sized countries, is that from 2021 you will effectively have a version of a European Super League that is more or less closed," he told Reuters.
Copenhagen said last week that talks between sides from Denmark, Scotland and Netherlands about an Atlantic League were ongoing.
"That is one of the initiatives these clubs have to examine," said Thomsen. "It's responsible management to examine the options.
"If this development doesn't change, it is also something the leagues will have a look at," he added.
"We will need to decide what to make room for in our calendar ... a competition from UEFA that we cannot participate in or a competition somebody else created. My guess is we will make room for the competition that creates the most value to Danish football."
PYRAMID SYSTEM
Thomsen said the whole pyramid system, in which clubs moved up and down and qualified for European competition based on their results, was at risk.
A previous attempt to form an Atlantic League involving teams from Portugal, Scotland, Sweden, Denmark, Belgium and Netherlands failed.
A similar plan for an international league was announced by clubs in Croatia, Serbia, Bosnia, Slovenia, Macedonia, Montenegro, Hungary and Bulgaria in 2011 but it also fizzled out.
"This is a very important moment in European football, this is about preserving values," said Thomsen.
"All of the football family, including UEFA and the biggest clubs, should take great care of these values because that's why we've been here for 100 years.
"Otherwise we will look into a future with different franchises competing against each other which would be a real shame for the game."
Thomsen, however, remained optimistic.
"My honest opinion is we will never get there because everybody will be able to see the value and the beauty of European football ... but it is a risk," he said.
(Editing by Tony Jimenez)
