The Tuareg-led Coordination for the Movements of Azawad (CMA) provoked the deadliest battle in almost a year between security forces and the rebellion as its fighters ambushed the central town of Lere on Wednesday.
"The provisional toll of the clashes is: armed forces -- nine dead, six injured, six hostages, one damaged vehicle," the ministry said in a statement.
"Enemy side: 10 dead and 16 injured, two vehicles destroyed; one vehicle, arms and ammunition recovered."
A foreign security source confirmed the fighting had stopped late on Wednesday, adding there was "no winner, no loser", with the rebels controlling the south of the town and the army dug in elsewhere.
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The attack came on a day of violence which started when militants opened fire on troops in the former Islamist stronghold of Goundam, 80 kilometres (50 miles) from Timbuktu, killing two soldiers and a child.
UN Secretary-General Ban Ki-moon blamed fighters from the CMA and called for an "immediate cessation of the hostilities in northern Mali" following "serious ceasefire violations".
A civilian source in an international team mediating peace talks between the government and the rebels said discussions were under way for "an exchange of prisoners between the two sides" following the battle for Lere.
"The meharists have rebel prisoners and the rebels have wounded meharist prisoners. Direct negotiations are under way to secure their release," the source said.
The CMA had warned on Tuesday it would assert its right to "exercise legitimate self-defence" after coming under attack from a pro-government militia.
The Tuareg were then sidelined by their one-time allies, extremists who imposed a brutal version of Islamic shariah in the region and destroyed historic buildings and artifacts in Timbuktu.