Kondogbia, who joined the Spanish club from Lens last summer, has been linked with a Premier League move - Arsenal and Chelsea have been tipped.
Real Madrid are another top Champions League team linked with the Frenchman, who impressed in his only season in La Liga so far.
And Emery has admitted that the 20-year-old could leave Sevilla this summer.
"We want him to stay here but there are circumstances that could lead to an exit," Emery told Spanish newspaper Marca.
"We will not make any movement to sell. There is no need to sell and we all know that in the club."
Kondogbia is under contract until the summer of 2017, and he made 31 appearances for Sevilla last term.
Arsenal are thought to be on the look-out for a deep-lying midfielder, having never replaced Alex Song after the Cameroon international departed for Barcelona last summer.
Chelsea were also thought to be in the mix for the midfielder, who was reportedly the subject of a £7.7m bid from a mystery club earlier last month.
The Blues currently have John Obi Mikel at the club, but the Chelsea midfielder has been linked with a move away from Stamford Bridge.
He also appeared at the under-20 World Cup in Turkey, playing for France and reportedly impressed watching scouts at the tournament.