Groups like hardline Islamists Ansar Dine, which encourage the application of strict Islamic law, consider shrines like the ones destroyed Saturday to be sacrilegious, Voice of America reported.
The group destroyed the tomb of 15th-century Muslim scholar Sidi Mahmoud and mausoleums in Timbuktu that led to UNESCO listing it as a World Heritage site, VOA reported.
"Every Friday all the people from Timbuktu usually go to the cemeteries in the early morning to pray," said Assoumane Maiga, a native of Timbuktu. "Today it's like you are taking a part of the soul of every single individual in Timbuktu."
Authorities in the capital city off Bamako called the destruction a war crime and vowed to prosecute the perpetrators, possibly in the International Criminal Court.
Ansar Dine had taken control over northern Mali from the country's interim government three months ago along with separatist group Tuareg National Movement for the Liberation of Azawad. Fighting in recent weeks has led to Ansar Dine pushing the Tuareg rebels out of Gao and Timbuktu, VOA reported.