A UN official said suspected jihadists took hostages at Le Campement Kangaba in Dougourakoro, adding there were casualties reported.
Residents living near the resort said shots were fired while smoke could be seen in the air.
Security ministry spokesman Baba Cisse said: "Security forces are in place. Campement Kangaba is blocked off and an operation is under way.
"The situation is under control."
Last week, the US Embassy in Bamako warned of an increased threat of attacks in Bamako.
The Foreign and Commonwealth Office advises against all but essential travel to the city.
Mali has been fighting a jihadist insurgency for several years, with Islamist fighters active in the country's northern and central regions.
In November 2015, at least 20 people died in a siege at the luxury Radisson Blu hotel in Bamako.
The attack was claimed by Al-Qaeda's North African affiliate, Al-Qaeda in the Islamic Maghreb (AQIM).
More follows...(c) Sky News 2017: Terror gunmen take hostages at luxury resort in Mali