The Pittodrie protege has turned down a new Dons deal and is expected to leave in the summer.
Aberdeen could be due compensation if Fraser does depart and Brown is keen for his club to be paid a fair amount for their work in developing the 18-year-old.
He said: "Far too many players are lost for minimal fees and Fifa needs to look at a fairer system.
"Top teams in England get more than £60million in television revenue.
"When there is that kind of money going around it is easy for them to come up here and take a chance on a young boy for a small amount of money. It is a cheap option for these clubs.
"Unless it is fairer then there is hardly a point in developing these boys.
"I would think I know Ally McCoist well enough that he would phone me and say he was interested in our boy.
"That is the impression I have, but I don't think we should be speculating about where Ryan's going. It is all right saying these young players should all be tied on lucrative long- term contracts.
"That would assume we had unlimited budget.
"We have got half a dozen promising youngsters and we would love to do that, but it's not always possible.
"Ryan Fraser only burst on to the scene this year."