Carlton, upset at losing Jarrad Waite for nothing, has taken aim at the AFL over its handling of free agency compensation and urged it to fix the flawed system.

Blues chief executive Steven Trigg said the club was expecting to receive a third-round selection for losing the key forward a to North Melbourne last week as an unrestricted free agent.

Trigg said the issue was deeper than the Waite decision and the AFL needing to review a "lack of transparency" in how it arrived at such decisions using a "mysterious formula".

Trigg's condemnation comes as the league prepares to announce what compensation - possibly pick No.3 - it will award Melbourne for the impending loss of James Frawley to Hawthorn.

"We are disappointed with the outcome and annoyed with the process, the process part in particular," Trigg said on Sunday.