Leon, the former world number 27, will become Spain's first female Davis Cup captain.
Nadal, uncle and coach to 14-times grand slam champion Rafa, sounded puzzled when asked about the appointment.
Leon's appointment could create problems "at dressing room level," he told Spanish radio.
"I have had zero relations with Gala Leon and I believe Rafa Nadal also zero, he has never mentioned it to me," he said.
"But it doesn't matter, I have never spoken to her but that doesn't mean anything.
"It would seem to be more normal if the captain had been someone like Juan Carlos Ferrero, or some ex-player of a certain level, which is what has happened recently."
Former world number one Ferrero, who retired in 2012, has expressed a desire to captain the team one day.
Moya quit after five-times winners Spain, fielding a weakened team, were relegated from the elite World Group for the first time in 18 years after a playoff loss in Brazil.
The RFET said in a statement on Monday that Leon, who quit the tour in 2004, would take on Moya's responsibilities as part of her role in charge of the federation's sporting management.
While Toni Nadal sounded unenthusiastic, Leon received support from Britain's twice grand slam champion Andy Murray who broke the mould earlier this year by deciding to employ former French player Amelie Mauresmo as his coach.
"Congrats to Gala Leon Garcia for becoming first female Spanish Davis Cup captain today... hopefully first of many," said the Scot on Twitter.
Moya stood down after less than a year in charge when Spain dropped out of the World Group, citing the unavailability of several top players as one of the factors in his decision.
Nadal did not play in Brazil because of a wrist injury that has sidelined him since Wimbledon. Spain's number two David Ferrer was also absent.
The RFET said full details of Leon's appointment would be disclosed on Tuesday in Seville.
(Reporting by Martyn Herman in London and Iain Rogers in Madrid, editing by Alan Baldwin)
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