The 22-year-old, the first white man to run under 10 seconds in the 100m, will concentrate on the 200 metres in which he is ranked fourth in the world this year and the 4x100 relay.
His coach Pierre Carraz told L'Equipe they had put a "definitive cross" against the 100 metres.
"In the results over 100m, Christophe is only ranked 10th among those who have entered," Carraz said. "Over 200m, we can hope for a medal."
Carraz said they could re-consider the decision to miss the 100 metres if there were significant withdrawals before the event which starts on August 4.
Lemaitre won the 100 metres at the last two European championships. He took the bronze medal in the 200 metres at last year's world championships in Daegu, South Korea and helped the French team claim silver in the sprint relay.