Gunmen killed at least five people including Malian soldiers in the attack on the Byblos Hotel in central town of Sevare, officials said.
According to reports, several suspected Islamist militants are thought to have died in the siege but the exact number of casualties is not yet clear.
Four bodies were found inside the hotel after the early raid in in the central town of Sevare, reported BBC.
Mali has been fighting Islamist rebels in the north for a number of years.
Suspected Islamist militants stormed the hotel on Friday after attacking an air force base in the town.
However, no group has claimed responsibility for the attack, but Islamist militants have claimed responsibility for other recent attacks in the south and centre of Mali.
Sevare, the major trading hub in Mali has faced attack like this for the first time.
The UN force in Mali took over responsibility for security in the country from French troops in July 2013.