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.
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.