However, the 23-year-old has missed Bayern's last two matches with a knee injury and Salihamidzic is refusing to let him join up with his national side while he recovers.
"We will notify the national teams that their players are not doing fine, that they are injured. Then the doctors will speak," he said.
The German champions are at risk of breaching FIFA regulations but Salihamidzic added both players will "definitely" not leave Bayern.
Bayern head coach Niko Kovac weighed in on the club-versus-country row after his side's 2-1 home loss to Hoffenheim on Saturday.
"We have our point of view and we have a duty to the players," Salihamidzic said. "If the players are diagnosed with an injury, it's clear that they cannot be used."
Hugo Lloris will also be missing for Deschamps’ side.
Spurs have not set a timetable for his return, but he is certain to miss France’s upcoming games and has already been replaced in the squad by Mike Maignan of Lille.
Maignan has been in the squad for the last five France games, but is yet to make an appearance.
As well as Hernandez and Lloris the World Cup holders will be without Paul Pogba and Ousmane Dembele, who are not fit enough to play.
N’Golo Kante will return to the national team setup, after missing out last time when he was unfit.