Al Shabab and Al Nasr face a play-off to enter the AFC Champions League next season after the Asian Football Confederation reduced the number of guaranteed places available to Pro League sides.
Al Ain, as Pro League champions, and President's Cup winners Al Jazira, are guaranteed participation in the competition next year.
But with just a week to go before the draw, last season's second and third placed sides - Shabab and Nasr - face having to enter at the qualifying stages.
Questions had been raised about Al Nasr meeting the necessary criteria to enter the competition, but now they will likely face a play-off against another nation's side to make their debut in the competition.
Australia has also seen its number of places in the competition limited, losing one place to leave it with one automatic qualifier and one play-off entrant.
The move has sparked anger in Australia, with Anthony Di Pietro, the Melbourne Victory chairman, warning the country's football chiefs must boost their ties with the AFC to avoid similar situations in future.
The decision means Perth Glory, which was due to take the third spot in next week's ACL draw, will now not be playing in the competition.
Tony Sage, the Perth chairman, has warned he decision could cost the club up to AU$80,000 (Dh306,000) in investments, and potentially damage its bid to lure David Beckham to the club.
Di Pietro said Football Federation Australia had been caught on the hop.
"I don't think we should accept this lying down. The FFA (Football Federation Australia) will regroup and look at what they can do, but from our perspective it's a very disappointing decision," he said.
Di Pietro added that he believed the Asian power brokers changed the criteria without informing the Australians.
"What we have to do in this country is understand the Asian Confederation and get more involved with it," he said.
"We need to get on committees, have interaction, get more involved with it. We need accountability and the right people to get overseas."
The AFC decided last week that Australia did not score sufficiently on benchmarks required to give a nation multiple guaranteed entries.
Instead, it cut the allocation of the 10-team A-League from two plus a qualifying tie spot to one plus a qualifying tie berth. Other countries get up to four representatives.
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