"The nomination had not been signed," said culture minister Aurelie Filippetti's office.
The announcement came amid rumours that Gayet, a divorced mother-of-two is four months’ pregnant with Hollande’s baby
Gayet's name had been listed on Villa Medici's website as recently as early on Wednesday.
The news of the appointment had first been reported on Tuesday after the actress's name had appeared on the institute's website.
Gayet's nomination had reportedly been put forward "before Christmas" by Villa Medici's director Eric de Chassey.
The Villa Medici jury allocates state grants to artists.