Brisbane boss Michael Bowers admits it is "disappointing" the AFL club became aware of alleged property transactions involving key players only after the deals were made.

Lions captain Jonathan Brown, Brownlow Medallist Simon Black and former football manager Graeme Allan have been linked to the deals.

The league's investigations manager Ken Wood is looking into the matter, to see whether the deals comply with strict AFL salary cap rules.

Channel Nine's The Footy Show is claiming several other former and current Brisbane players are also now involved in Wood's inquiries.

Allan left the Lions this year to take up a key role with expansion club Greater Western Sydney.

"We had conversations about that, I certainly made 'Gubby' (Allan) aware I'd like to know before these things happen," Bowers told The Footy Show.

"If you're going to the AFL advising them of something, it's a lot better than reading about it in the paper.

"It is a disappointing thing from our point of view that happened."

There were newspaper allegations last month that Brown and Black had bought property five years ago in Noosaville and that Allan was involved.

"We'd like to be involved a lot earlier in the process," Bowers said.

"I suppose the curious thing about all that was that Simon and Jonathan bought properties and for some reason Jonathan sold it at a loss.

"If it's a salary cap issue, the numbers are going the wrong way.

"But Ken is going to have a look at it, we have no problems with that, we'd just love to be involved before the transactions."

The AFL has promised much tighter control of third-party player payments as the game heads to limited free agency.

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