The girl's mother at first tried to pursue the kidnappers, who scaled a wall with her child, but then turned back to protect her second daughter, also an albino.
"We searched for the little girl everywhere. We found her body beside a mosque, but she had no head," said a village teacher, Oumar Diakite.
Blaming a lack of security for the killing, angry local residents on Sunday partially burned down the paramilitary police headquarters in Fana, according to several witnesses.
"We demand justice. Her head was taken. This is a ritual crime," activist Mamadou Sissoko told AFP after going to the scene.
Sissoko, the general secretary of the Federation of Associations of Persons with Albinism in West Africa (FAPAO), pointed out the link between crimes against albinos and political events, ahead of Mali's presidential election on July 29.
"Every time there are elections, we become prey for people who want to make ritual sacrifices. This is not the first time this has happened in Fana," he said. "The state needs to take up its responsibilities."
An albino legend on the international stage, Malian musician Salif Keita has for years campaigned for the protection of albinos, who are both stigmatised and hunted for ritual purposes in many African countries, including Malawi, Mozambique, Tanzania and Zimbabwe as well as in West Africa.
Dozens of albinos are attacked and killed every year by people prepared to hack off their limbs to use in rituals aimed at bringing wealth, success and good fortune.
Albinism is a genetic hereditary disorder that causes a partial or total absence of pigmentation in the skin, the hair and the eyes, so that sufferers have a bleached look.
Apart from discrimination, albinos are also exposed to problems of eyesight and a heightened risk of skin cancer. In Africa, protective suntan creams are hard to find and expensive.