Mali in January called in military support from former colonial power France. Control over northern Mali fell to Islamic militants, including al-Qaida, following an early 2012 coup.
French and Malian forces have since liberated key cities, including Timbuktu and Gao. Gunfire was reported in Timbuktu, however, as government forces fought with remaining Islamic militants.
Militants managed to get back into the city following a suicide bombing last weekend. Timbuktu Mayor Ousmane Halle told The New York Times by telephone that the security lapse was regrettable.
"They had said Timbuktu was secured," he said.
No group claimed responsibility for militant operations in Timbuktu. Al-Qaida last year razed historic religious sites in the city because they weren't in line with the group's conservative views on Islam.
Reports of the security situation in Timbuktu were mixed by Monday afternoon.
U.N. Secretary-General Ban Ki-moon last month called for an African force to integrate into a U.N. mission that would replace French forces in Mali. A French combat and counter-terrorism role would be needed to support a U.N. mission, however.