UEFA said any potential Champions League ban for RasenBallsport Leipzig or Red Bull Salzburg for having the same owner is "hypothetical" until the qualifying places have been decided at the end of the season.
Austrian daily Salzburg Nachrichten reported on Wednesday that European football's governing body UEFA had offered a "early signals" that one of the two clubs - both owned by Austrian energy drink giant Red Bull - would be prevented from playing in the Champions League, should both qualify.
Both RasenBallsport Leipzig, enjoying a marvellous debut campaign in Germany's Bundesliga, and Austrian Bundesliga leaders Red Bull Salzburg are on course to qualify for the Champions League based on their current league positions.
A total of 22 teams automatically entered the 2016-17 UEFA Champions League group stage with the remaining slots taken by the 10 sides who come through qualifying.
A UEFA statement said: "We cannot comment at this stage on what is a hypothetical question.
"(There will be) more concrete information from the beginning of June, when the list of participating clubs taking part in UEFA European competitions is published."
Article 5 of UEFA's European Competitions Regulations states "no club participating in a UEFA club competition may, either directly or indirectly hold or deal in the securities or shares of any other club participating in a UEFA club competition".
In the case of multiple teams with the same owners qualifying, only one of them would be admitted to a UEFA club competition, it said.
Oliver Mintzlaff, global head of soccer for Red Bull and RB Leipzig CEO, was quoted as telling German news agency SID: "If we qualify there is no reason why we should have any doubts about playing in Europe next season."
A spokesman for Red Bull Salzburg said: "Even UEFA said that any resumption regarding this topic is only speculation - nothing more. And FC Red Bull Salzburg are not willing to take part in any kind of speculation."
(Reporting by Ed Dove; Editing by Alison Williams)