Conditions had eased since the weekend but forecasters said more rain was on the way.
"We appeal for careful movement by the rivers and ravines due to extraordinary water levels," the Hydrometeorological Service said.
Earlier downpours left more than 300 homes inundated, the Crisis Management Centre (CMC) said.
In the city of Kicevo, about 65 kilometres (40 miles) southwest of the capital Skopje, around 250 people had to leave because of flooding, the CMC said.
Recovery efforts were underway in the city on Monday, with firefighters and government workers clearing streets and pumping water from buildings, including a hospital.
Landslides in the western city of Tetovo also forced rescue teams to work through the night, the CMC said.
According to the Red Cross over 1,200 people had been affected by the storm nationwide.
Vast areas of farmland in the country's north and western regions remained submerged.
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