Karl Robinson claims the introduction of the Elite Player Performance Plan shows a lack of respect for Football League clubs by those in the Premier League.
Clubs are now guaranteed more funding for their youth system over four years but they are set to receive less money if players under the age of 17 depart for a new team.
"I am disappointed with this new ruling that means we're probably going to lose an awful lot of players," the MK Dons boss told Sky Sports.
"I think it lacks respect for the Football League clubs.
"The Premier League is one of the biggest leagues in the world and we respect them immensely.
"I just don't think it's very fair on clubs that are working hard to produce players that we can lose them for such a small price.
"We sold Sam Baldock (to West Ham) for over £2million and we rely on that income to survive.
"It's happened now (the introduction of the EPPP) and we've got to find a way round it and still keep the young players at this football club."
Robinson is certain the Dons will continue with their successful youth set-up and he is full of praise for the work chairman Pete Winkelman has done to develop young players.
"We always will because we believe in it," he said when asked if MK will continue to give chances to promising youngsters.
"The chairman is a great chairman to work for and he believes that is the sole aim of the football club to produce players for the first-team."