Cardiff have been ordered to pay French club Nantes six million euros (around £5.3million) in relation to the signing of Emiliano Sala in January.
The Argentinian died when the aircraft he was travelling in from France to the UK to complete his move to the Welsh side crashed in the English Channel.
The Bluebirds had argued that they could not be held liable for the £15million fee because Sala had not registered as a Premier League player.
But FIFA's player status committee has decided that they must pay the amount equivalent to the first instalment of that fee.
A statement from the committee read: "In a meeting held on September 25, 2019, the FIFA players' status committee established that Cardiff must pay Nantes the sum of 6,000,000 euros, corresponding to the first instalment due in accordance with the transfer agreement concluded between the parties on January 19, 2019 for the transfer of the late Emiliano Sala from Nantes to Cardiff.
"The FIFA players' status committee, which never lost sight of the specific and unique circumstances of this tragic situation during its deliberations on the dispute at stake, refrained from imposing procedural costs on the parties.
"The findings of the decision were notified to the parties concerned today. Within a deadline of 10 days, Cardiff and Nantes can request a copy of the grounds of the decision, which can be appealed to the Court of Arbitration for Sport in Lausanne."
The aircraft carrying Sala and British pilot David Ibbotson crashed on January 21.
The body of Sala was recovered and he was formally identified by Dorset Police in February.
It is understood Cardiff were prepared to appeal the verdict at the Court of Arbitration for Sport if they were ordered to pay a fee.
A report from the Air Accidents Investigation Branch (AAIB) which was published in August found that Sala had a high concentration of carbon monoxide in his bloodstream prior to the plane crash.