The 19-year-old female, Daniza, was knocked out so that she could be transferred to a more remote part of the Trento region of northern Italy, a spokesman for the provincial government said on Thursday.
"The bear was put to sleep but, unfortunately, did not survive," he said. An autopsy has been ordered to establish the cause of death.
Environment Minister Gian Luca Galletti said he had asked the region for an explanation. "We have to be sure this does not happen again," he said. "These bears have to be monitored and protected."
Carla Rocchi, the chair of the Italian Association for the Protection of Animals (ENPA), added: "This didn't happen by chance or by accident. It was 'animalcide'."
Local officials had been trying to capture Daniza since August 15th, when she injured Daniele Maturi, a local man who chanced upon her and her two cubs in woods near the small village of Pinzolo, sparking a national debate over the wisdom of efforts to conserve a colony of bears in the Alps.
Local officials said they had no option but to ensure human safety, while environmentalists argue that Daniza was being punished for following her natural instinct to defend her young.
Angelo Bonelli, a spokesman for Italy's Greens, called for a criminal probe into the bear's death.
"A bear that was attempting to defend her own cubs from danger has died at the hands of the institutions, and now her small cubs are also in danger without the protection of their mother."
One of Daniza's cubs, who was captured with her, was tagged and released back into the wild. The whereabouts of the other one was unknown. The cubs are around eight months old.
"The situation of the cubs is particularly worrying," ENPA wildlife specialist Andrea Brutti told AFP. "Up until three or four years old they need their mother to teach them."
Daniza is one of a number of bears who have been introduced into the Italian Alps under an EU-funded programme "Life Ursus." There are thought to be around 50 living in Italy.