The French U21 player was withdrawn after 41 minutes during their 1-0 win over Belarus, with the 21-year-old sustaining damage to his groin.
Scan results have shown that he could be out for up to two months, with Rennes manager Philippe Montanier believing Ntep's injury came as a result of two games in four days.
"This is a bad blow for the team and the group," Montanier said.
"When you are a young player, playing 90 minutes on Saturday (against Valenciennes) on a difficult pitch and then on Tuesday, this is not such a surprise.
"But we can't do anything. They are at the disposal of the national team."