Sala and his pilot David Ibbotson have been missing since shortly after their plane took off from France on January 21.
The Bluebirds have withheld the first scheduled payment until they are satisfied with the documentation.
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A source at Cardiff says they will honour the contract, but not until they have clarified "all the facts".
The Piper Malibu N264DB which was carrying Sala and Ibbotson has recently been found with one body among the wreckage, but it has yet to be identified.
Although Nantes were entitled to the first instalment of Sala's fee by now, Cardiff have been left surprised by the demand given the circumstances and the timing.
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The two clubs had agreed on a payout in three instalments, which is relatively common in big transfers.
The situation is further complicated as French club Bordeaux are also due 50 per cent of the reported £15m transfer due to a clause inserted when Sala joined Nantes in 2015.
Sky Sports News understands the club feels it necessary for the salvage operation in the Channel to be concluded and for both the Air Accidents Investigation Branch (AAIB) and the police to conclude their investigations before any payments are made.
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Cardiff is looking into details about who owned the plane and who insured it as investigators work through weather difficulties to recover the body that's been seen inside the wreckage, and they intend to meet their transfer obligations to Nantes, according to the Mirror report.