The news, based on information from persons directly involved with the conservation of the historic texts, came as a relief to the world's cultural community which had been dismayed by varying media reports of widespread destruction of the priceless manuscripts.
After French and Malian troops on Sunday retook Timbuktu, a UNESCO World Heritage site and ancient seat of Islamic learning, from Islamist insurgent occupiers, the city's mayor reported the fleeing rebels had set fire to a major manuscript library.
But experts said that while up to 2,000 manuscripts may have been lost at the South African-funded Ahmed Baba Institute ransacked by the rebels, the bulk of the around 300,000 texts existing in Timbuktu and its surrounding region were believed to be safe.
"I can say that the vast majority of the collections appear from our reports not to have been destroyed, damaged or harmed in any way," Cape Town University's Professor Shamil Jeppie, an expert on the Saharan city's manuscripts, told Reuters.
A Malian source also directly involved with the conservation of the Timbuktu manuscripts told Reuters 95 per cent of the total documents were "safe and sound".
The two sources said that soon after Tuareg rebel fighters swept into Timbuktu on April 1 in a rebellion later hijacked by sharia-observing Islamist radicals, curators and collectors of the manuscripts had hidden the texts away for safety.
"They had shipped them out and distributed them around," Jeppie said. The Malian source, asking not to be named, said the manuscripts had been concealed "a little bit everywhere".
Some of the mansuscripts that constitute Timbuktu's "treasure of learning" date back to the 13th century.
Brittle, written in ornate calligraphy, and ranging from scholarly treatises to old commercial invoices, the documents represent a compendium of human knowledge on everything from law, sciences and medicine to history and politics. Some experts compare them in importance to the Dead Sea Scrolls.
The Ahmed Baba Institute, a Malian state library, is named after a Timbuktu-born contemporary of William Shakespeare and housed more than 20,000 ancient scholarly manuscripts.
Timbuktu was liberated by French and Malian forces as part of a rapid French-led military offensive launched on January 11 that drove fighters from the Islamist alliance occupying Mali's north back into the desert and mountains near the Algeria border.
French troops have taken control of the airport in the northern Malian town of Kidal, the last rebel stronghold in the north.