Nantes referred the matter to Fifa after the English Premier League side declined to pay an initial six million euros from the total fee of 17 million euros.
"Nantes have naturally turned to Fifa. We have bodies which can deal with these sorts of things," said Fifa boss Gianni Infantino. "There's also a human aspect to the situation which makes us more than just sad. It's a tragedy.
"Fifa will take care of it and I hope both clubs will come to an agreeement."
Cardiff were due to pay the initial sum once the transfer had been registered but the club said they wanted to wait for the results of the investigation into the accident before transferring any money.
"Cardiff City remains committed to ensuring fairness and accountability with respect to the agreement between Cardiff City and FC Nantes," said a Cardiff City statement.
"But first and foremost the relevant authorities must be allowed to determine the facts surrounding this tragedy. It is inappropriate to comment further at this stage."
According to Nantes, Sala's move from France had been completed and an International Transfer Certificate (ITC) issued.
As the ITC had been registered and Sala thus confirmed as a Cardiff City player, according to Nantes, the Welsh club were obligated to pay for the transfer of the striker.
Cardiff say they are concerned about possible irregularities involving the flight from Nantes to Cardiff which resulted in Sala's death.
Britain's Air Accidents Investigation Branch said on Monday that the plane carrying Sala did not have a commercial licence.
But it said the journey would have been allowed as a private flight in which costs are shared between pilot and passenger. It added that the basis on which Sala was a passenger had not been established.