Al-Qaeda-linked insurgents seized Timbuktu -- around 1,000 kilometres (600 miles) northeast of Mali's capital Bamako -- alongside the west African nation's other desert towns and cities in 2012.
They wrecked 16 of its shrines to Muslim saints that date back to the ancient caravan city's 15th and 16th century golden age as an economic, intellectual and spiritual centre.
"UNESCO has involved the International Criminal Court with the destruction of the mausoleums," Irina Bokova, the organisation's general director, told reporters at the end of a visit to Timbuktu.
The mausoleums are designated as World Heritage monuments by UNESCO, and Bokova said destroying cultural heritage was considered a war crime under the UN's 1954 Hague Convention.
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The UN cultural body began rebuilding Timbuktu with the Malian government and other international organisations after a 2013 French-led military operation drove the jihadists out of the city.
The reconstruction, which started last year, relies heavily on traditional building methods and cultural knowledge of the area, generating around 140 local jobs.
"It is through the reconstruction of mausoleums that we can accompany the peace agreements and restore the identity of the city... We will also help renovate other riches of Timbuktu cultural heritage," Bokova told reporters.
The mausoleums were constructed to pay homage to deceased saints who were regarded as pious, great humanists and scholars of their time.
For the people of Timbuktu -- dubbed the "city of 333 saints" -- their destruction was an assault on Malian history and culture.
But 370,000 of these priceless parchments were smuggled to Bamako in 2012 to protect them from the jihadists and archivists in Mali's capital are now painstakingly classifying and digitising them.