The warning came amid the resurgence of the virus in some foreign nations after the relaxation of lockdowns and reopening business activities, reports Xinhua news agency.
He called on the authorities to keep and step up precautionary strides in facing the threat.
"We must keep on alert over the possibility of the second wave and anticipating it," Jokowi told a limited cabinet meeting.
The warning came after the head of state conveyed the country's convincing economic growth prospect with an estimate of 5.4 per cent next year as predicted by the International Monetary Fund.
"I think this is a high growth projection, and should this be materialized, it suggests that our economy will accelerate at the fastest pace among the global economic expansion," he said.
Indonesia has recently eased restrictions applied to curb the virus spread along with the resumption of business activities and the reopening of tourist destinations under tight health protocols.
The spread of the COVID-19 virus in Indonesia has been afloat with daily cases reaching over 1,500, emboldened by the enlargement of red zones or high-risk areas, still the upbeat over the vaccine availability for usage early next year helped offset the concern, according to the COVID-19 Task Force.
The number of red zones reached to 53 this from 35 and the number of orange zones jumped to 185 from 169 a week earlier, the country's COVID-19 Task Force said on Monday.
Indonesia has so far reported a total of 100,303 COVID-19 cases, with 4,838 deaths.