Murray Magpies and Billabong Crows are the only two sides in the competition not to have a full contingent of junior football sides this season.
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Clubs were given until the end of round four before informing league officials of their stance for the remainder of the season.
The Magpies won't have thirds or fourths while the Crows will also be without thirds.
League president Phil Bouffler said a lack of junior numbers was an issue nationwide.
"This is not an issue isolated to just our league or clubs and is happening across the board," Bouffler said.
"It could have been worse but even if a couple of clubs are missing junior sides it is still far from ideal.
"As a league we have to try and help these clubs get their juniors back.
"It becomes problematic without juniors because with the points system you need your local talent filtering into the senior ranks because they are one-pointers.
"I know Murray Magpies have re-established Auskick which they haven't had for a while and is a step in the right direction.
"Sometimes the problem is just cyclic and you have a lot of junior girls coming through and not boys and vice versa.
ALSO IN SPORT
ALSO IN SPORT
"But the AFL needs to address this issue, that's what needs to happen.
"As I said, it's a nationwide issue and there is just not the number of juniors coming through that there have been in the past.
"What the reason is for that - I don't have the answer but someone smarter than me needs to find out."
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