France are already without first-choice centre back Raphael Varane, who was ruled out of the tournament earlier this week, and fellow central defender Mamadou Sakho following his suspension for failing a drugs test last month.
"I would have preferred to have less problems, but they are there and I'm managing them the best way possible," Deschamps told a news conference.
The French squad, which will be pared down from 31 to 23 by Sunday, take on Cameroon in a friendly in Nantes on Monday.
Varane was replaced in the squad this week by Sevilla's Adil Rami, who has not played for the national team for three years despite previously winning 26 caps.
Deschamps appeared to suggest that Mathieu, who picked up the injury during the King's Cup Final at the weekend, was not at risk of missing the start of the tournament on June 10.
"He felt he had a problem with his calf. It's not serious as such, but I will wait a few days to get more details. He won't be available for (the game) in Nantes," he said.
Les Bleus take on Romania, Albania and Switzerland in Group A at the European Championship finals on home soil, beginning on June 10.
(Reporting By John Irish, Editing by Neville Dalton)
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