"Over the course of the operation, a total of more than 87,500 rebels have been eliminated, 1,411 settlements have been liberated and more than 95 percent of Syria's territory," Shoigu was quoted as saying at a forum in Singapore in a ministry statement.
"Most of the rebels have been liquidated," Shoigu said.
Britain-based war monitor the Syrian Observatory for Human Rights says close to 365,000 people have been killed during the seven-year civil war.
Russian air forces have carried out more than 40,000 bombing missions, hitting about 120,000 targets of "terrorist" infrastructure, Shoigu said.
The defence minister said that "Syrian armed forces currently control territory where more than 90 percent of the population lives."