Bolton boss Owen Coyle is keen to bring the 30-year-old striker back to the Reebok Stadium after Klasnic impressed on loan last season.
The Croatian scored eight goals in the Premier League and talks had taken place regarding another season-long loan arrangement.
The wages Klasnic was receiving at Nantes were understood to be a stumbling block for Bolton in any potential deal, but a statement on the French club's website said: "He came free. He leaves free. FC Nantes and Ivan Klasnic reached an agreement on Sunday evening to resolve the contract linking them.
"FC Nantes and its leaders would particularly like to thank Ivan for his professionalism and his human qualities. We wish him success in the rest of his career."
Coyle recently told the Bolton News: "I have said all along that if we can get something sorted financially with Ivan, then I would love to have him back at the football club.
"But finance does play a part - and without getting into the bits and pieces, he's on a fantastic contract at his club. That's the only thing standing in our way, nothing else.
"I think Ivan is a top class player who will score goals in my team. But if it's too rich for the football club, it's too rich."