Kewell left Elland Road for Anfield in the summer of 2003 in a deal which perplexed Whites fans.
Leeds received barely £2m from the £5m deal with £2m going to Max Sport, the company run by Kewell's advisor and mentor Bernie Mandic.
But Lineker insisted that Mandic was not a licensed agent and, as such, clubs were not allowed to deal with non-licensed agents.
Lineker said: "Both Liverpool and Leeds are in clear breach of the FIFA guidelines on that. It's a fact. Clubs cannot negotiate with a non-licensed agent. Leeds were in a desperate negotiating position and Mr Mandic was in a position of great strength, which he used for himself very well.
"I have no reason to have a go at Harry Kewell for anything other than being a pawn in a murky deal. It's his transfer deal. If an agent is walking away with £2 million, the player should be asking questions, the why and justification of that fee. He wasn't interested and he has to be criticised for that..."