The ECA, whose members include all of the continent’s biggest clubs, is working with UEFA to redesign European competition from 2024.
The ECA plan, according to European Leagues officials who have seen it, foresees a three-tier league with promotion and relegation between each tier.
The top tier, with 32 teams, would be the new version of the Champions League and would allow the top 24 teams to keep their places for next season, ending the tradition that qualifying for European competition is achieved via national leagues.
In the three tiers overall, 40 teams would stay in the league for the following season - regardless of their performance in domestic competition.
"What has been really disappointing so far has been the whole conversation has been driven by representatives of the big five leagues," Agnelli told an ECA general assembly in Malta.
"And I see it as a protectionism of the big five leagues vis-a-vis the rest of European football.
"The whole principle of access is about addressing stability. It's why I talk about a principle of 40 teams remaining in the system. It's not about tier one (the Champions League)."
Europe's domestic leagues argue that they would be dramatically weakened by the plan which would in effect be close to a European Super League.
Agnelli gave Ajax Amsterdam, surprise semi-finalists in the Champions League this season, as an example, pointing out that the Dutch side only enter European competition in the qualifying rounds.
"How can Ajax grow?" he said, suggesting that a guaranteed place in European competition would help them and clubs of a similar stature.
"It's about team number 16 to team number 40-50 in the club coefficients. Those are the clubs that carry the biggest risks in not being able to grow in a European system because of the current access system."
Agnelli urged clubs to "see things from a different level".
"We as Germans, have to think: 'What are the issues of the Polish?'. We as Italians, we must think: 'What are the issues of the Greeks?," he said
"We should try to put ourselves in the shoes of each other and understand what is the best solution going forward."
(Reporting by Brian Homewood, editing by Ed Osmond)
