A decision to that effect was made by majority vote on Wednesday.
The tribunal's Registry ordered Praljak on August 22 to return within 90 days nearly EUR 3.3 million which the ICTY paid for his defence after finding out that Praljak had enough money to pay for his own defence.
Praljak's lawyers said he would appeal the Registry's decision.
After that decision, the trial chamber changed the terms of Praljak's provisional release by making them stricter, ordering that he must stay at his home in Croatia under tighter supervision.
The prosecution objected to that decision, saying the provisional release must be revoked, as it increased the risk of flight.
Praljak told the tribunal he would rather return to Scheveningen than stay under house arrest.
Praljak is accused of crimes committed as part of a joint criminal enterprise led by former Croatian President Franjo Tudjman to ethnically cleanse Bosnia and Herzegovina's Herceg-Bosna region and annex it to Croatia.
Praljak and the others accused in the case surrendered to the ICTY in April 2004. He has been under provisional release since December 21, 2011, waiting for a decision to be handed down in the case towards the end of the year.