Turkish-based group Doyen Sports Investment hold 50% of the Frenchman's rights after helping Los Rojiblancos acquire him from Lens last summer.
The midfielder has impressed in La Liga this season, leading to links with Manchester City, Real Madrid, AC Milan and Inter Milan.
A deal is believed to be in place that states Sevilla must purchase the remaining rights from Doyen at half the price of any bid that they receive over the €6m fee.
However, Del Nido said that such agreements are commonplace and insisted that the club are not looking to offload the 20-year-old.
"Sevilla hold 100% of Kondogbia's rights," Football Espana quotes Del Nido as saying.
"No-one can talk to the player without our permission and he has four-and-a-half years left on his contract.
"It is true that with an offer of €6m, Sevilla are required to negotiate buying the remaining 50% [from Doyen], but this has been the case with many players when they have come to be sold on."
Kondogbia has won one cap for the French Under-20 team.