"Ongoing attack at Hotel Kangaba "Le Campement" 30 min southeast of #Bamako, #Mali", the department tweeted, warning people to avoid the area.
'There were four national police vehicles and French soldiers in armoured vehicles on the scene'.
There was no immediate claim of responsibility for the attack, which came amid the final week of the Muslim holy month of Ramadan.
It has been targeted constantly by jihadists, with dozens of peacekeepers killed, including five on Saturday.
Col. Diarran Kone, a spokesman for the Malian army, said eight others were wounded in the attack on the military base about 80 km (50 miles) from Timbuktu.
As night fell, witnesses saw smoke rising from the Campement Kangaba, which features three swimming pools and is a popular escape from the Malian heat.
A local resident earlier described the grim situation before security forces arrived, saying there were "no Malian soldiers to be seen - the camp has been laid waste".
Mali has been fighting a jihadist insurgency for several years, with Islamist fighters active in the country's northern and central regions.
The UN has a 12 000-strong force known as Minusma in Mali, which began operations in 2013.
In November 2015, at least 20 people died in a siege at the luxury Radisson Blu hotel in Bamako. A devastating attack on the Radisson Blu Hotel in Bamako later that year left 20 dead - six Malians and 14 foreigners. Germany has considered sending troops to the strife-torn country.
There were no details of casualties but the attack was continuing on Sunday evening (Monday morning NZ time).
Al-Qaeda linked jihadi factions hold large swathes of desert in northern Mali, after hijacking an uprising by ethnic Tuareg rebels who launched an advance in 2012, bolstered by the free flow of militants and weapons from the Libyan civil war.
But jihadists have continued to mount numerous attacks on civilians and the army, as well as on French and United Nations forces still stationed there.