The man appointed police chief by the Islamists, Aliou Mahamar, told RFI that Abdoul Malick Maiga had been beaten on his orders and left outside the hospital.
Hundreds of residents protested against Maiga’s detention on Sunday night, setting light to Mahamar’s car.
Doctors say that Maiga regained consciousness overnight but was still in “intense pain”.
Earlier on Sunday protesters packed Gao’s Place de l’Indépendance and prevented the Movement for Oneness and Jihad in West Africa (Mujao), which controls the city, from cutting off a thief’s hand.
Local people say that the accused was a young Mujao member who had stolen weapons in order to sell them.
"We don't want to know what this young man did, but they are not going to cut his hand off in front of us," a resident said on Sunday.
Gao residents have resisted the imposition of Mujao’s interpretation of Islamic sharia law and violent protests in May left one person dead.
Mujao’s punishments include “25-50 lashes for less serious crimes, for theft they cut off your hand, for adultery it’s stoning”, one resident told RFI.
Another Islamist group, Ansar Dine, stoned a couple to death in the town of Aguelhok last month.
The Malian government on Monday condemned the attack on Maiga and claimed that the events showed “inability of the occupiers to impose their destructive law and their dubious faith on a population that unequivocally rejects their presence”.