About 300,000 texts at the government-funded Ahmed Baba Institute escaped destruction, Discovery News reported.
Up to 2,000 manuscripts may have been destroyed, said Mahmoud Zouber, Mali's former presidential aide on Islamic affairs.
During the 10 months the Islamist radicals occupied Timbuktu, Malian preservationists moved thousands of documents, some of which dated to the 12th century, out of the institute into hiding places around the city and surrounding areas, authorities dais.
Several mausoleums of Islamic saints did not fare so well, Radio France Internationale reported.
Local journalists said about a dozen of them were destroyed by the fundamentalists, who considered rites at the burial sites to be "idolatry."