The Bundesliga champions saw off last season's runners-up Juventus in the round of 16 to book their ticket for the quarter-finals and Rummenigge feels it would be in football's best interest if UEFA came up with a system to keep the big teams apart as long as possible.
"What I don't like about the Champions League draw for the knockout stages is that it all depends on fate," Rummenigge told reporters.
"UEFA should consider an alternative with seeded teams or something similar.
"I saw some games in the first knockout stage where I came close to switching off the TV.
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"And now we see a team like Juventus - who made it to the final last season - crash out in the round of 16.
"This is no longer acceptable. I am fed up with how fate plays such a big role."
UEFA currently already has a system in place where group-stage winners cannot be paired with other pool winners - or with a team from the same country - in the round of 16 in order to protect the big teams.
Juventus' failure to finish top of their group saw them paired with Bayern, while Manchester City - who beat Massimiliano Allegri's men to top spot - were drawn with Dynamo Kiev.