Scott Boras has routinely made millions for his clients in free agency, but a change in the compensation rules this year has the super agent questioning the fairness of the system.

Under compensation rules instituted this offseason, Major League Baseball teams had the option of offering $13.3 million qualifying offers to any of their pending free agents who spent the entire 2012 season with that team. If a player declined the offer and signed with another team, the player's new team would have to forfeit its highest draft pick (except top-10 picks, which are protected) and the signing-bonus allocation slotted to that pick.

"When you have a system that does not reward performance, you know we have something corrupt in the major league process," Boras told FoxSports.com on Monday. "You cannot have that in the major league system, because it's not rewarding performance."

Before the current system, free agents were assigned a Type A or Type B designation based on Elias Sports Bureau ratings. Type A and B players who declined arbitration were tied to draft pick compensation, but teams didn't face the loss of signing-bonus allocation for signing those players.

So under the current system, fewer free agents were tied to compensation, but Boras told FoxSports.com that the bonus penalty of the new system damages the market value of free agents who received and declined a qualifying offer.

Boras told FoxSports.com that the new system forces major league teams to choose between making improvements to the big league team or focusing on improving through the draft.

Boras made his comments on the same day client Kyle Lohse signed a three-year, $33 million deal with the Milwaukee Brewers. Lohse remained unsigned until the end of March in part because of the draft penalty associated with signing him.

"They have to allow teams to spend whatever they want to spend in the draft, so draft dollars aren't viewed as more important than [the major league team's] performance," Boras told FoxSports.com.

In all, nine free agents (Josh Hamilton, B.J. Upton, Nick Swisher, Rafael Soriano, Hiroki Kuroda, David Ortiz, Michael Bourn, Adam LaRoche and Lohse) received a $13.3 million qualifying offer from their teams, with each declining the offer.

Kuroda (one-year, $15 million with the New York Yankees), Ortiz (two-year, $26 million with the Boston Red Sox) and LaRoche (two-year, $24 million with the Washington Nationals) ended up re-signing with their former teams. Hamilton received a five-year, $125 million deal with the Los Angeles Angels and Upton got a five-year, $75.25 million contract with the Atlanta Braves. Soriano signed with the Nationals on a two-year, $28 million deal.

The Cleveland Indians signed both Swisher (four-year, $56 million contract) and Bourn (four-year, $48 million). Bourn, however, remained unsigned until the middle of February.

Boras represents three of the players who received qualifying offers (Lohse, Bourn and Soriano).