A building housing over 60 thousand manuscripts from the ancient Muslim world and Greece was set aflame, raising fears of further damage to the country's cultural heritage after months of destruction by Islamists.
French paratroopers tried to block fleeing hardliners as ground troops coming from the south seized the airport of Timbuktu, which has been a bastion of the jihadists controlling the north for 10 months.
"We control the airport at Timbuktu," a senior officer with the Malian army told journalists. "We did not encounter any resistance."
French army spokesman Colonel Thierry Burkhard said the troops, backed up by helicopters, had taken less than 48 hours to seize control of the so-called Niger Loop between Timbuktu and Gao.
Timbuktu mayor Halley Ousmane, who is in Bamako, confirmed the fire at the Ahmed Baba Centre for Documentation and Research, which housed between 60,000 and 100,000 manuscripts, according to Mali's culture ministry.
"I spoke to my media officer this morning. What has happened in Timbuktu is dramatic," he said.
Ousmane said he had also been informed that Islamists had "burnt alive" a resident who had cried out "Vive la France".
The Ahmed Baba institute was set up in 1973. A new building was opened in 2009 following a bilateral agreement with South Africa to promote the conservation, research and promotion of the manuscripts as African heritage.
Italian Prime Minister Mario Monti on Monday indicated Rome was scrapping plans to provide logistical support for French-led forces in Mali due to a failure among the main parties to reach a political deal ahead of elections next month.
"I asked the leaders of the three parties of the majority to give their views but we did not receive the support we had hoped for," Monti, who is himself running as leader of the coalition of centrist parties, said in an interview with La7 television.
Defence Minister Giampaolo Di Paola last week said Italy would send a refuelling plane and two transport planes to carry troops and equipment in the conflict against Islamist-led rebels in Mali.
While expressing Italy's "strong support" for the operation, however, Foreign Minister Giulio Terzi said that "internal political conditions" meant Rome could not offer concrete backing at the moment.
It was not immediately clear whether the change of heart would also include the group of 15 to 24 instructors that Italy is planning to send as part of a European mission to train Malian troops.
Meanwhile, a spokesman for British Prime Minister David Cameron said on Monday that London was "keen" to contribute more in addition to two transport planes and a
surveillance aircraft which have already been provided.