The Italian fell heavily in the second session in Germany at the weekend and scans have since confirmed he has a broken right tibia and fibula.
The injury will need surgery and the 24-year-old is likely to miss the final two rounds of the season.
"A bad day for Canepa and for all of us,” team manager Andrea Petricca said. “Everything seemed to be going well and we were preparing for the Superpole when Niccola fell. I personally accompanied him to the hospital and he was found to have a double fracture of tibia and fibula of his right leg.
“We are very saddened by what happened. Unfortunately I do not think that he will take part in the remaining two races of the season. We do not want to think about his replacement yet, only to make sure that Niccola receives the best care possible.”
The season draws towards a conclusion with races in Portugal and France.