Winds from the storm -- which mainly hit the western and northwestern part of the country -- were clocked at 72 to 80 kph (44-49 mph).
In one day or less, some residents experienced more than three times the rainfall they normally receive in a month, CNN meteorologists reported. More rain is possible in the region, with a significant chance for showers during the rest of this week.
Most of the flood victims were found in the villages of Stajkovci, Singjelic, Smilkovci and Aravinovo near the capital, Skopje, according to the state-run Macedonia Information Agency, or MIA. The dead included a child, age 7 or 8.
MIA earlier had reported that six people were missing in the disaster, but so far no updates have been provided.
Workers have set up emergency response centers to assess the flood damage.
Landslides from the storms have left about 70 vehicles unable to move on highways, MIA reported.
Nikola Steriov, a nongovernmental organization worker who lives and works in central Skopje, isn't blaming the weather so much as the nation's infrastructure's ability to handle it.
"Infrastructure is not good enough for this kind of rain," he said.
In affected areas, Steriov said, "People weren't getting the help they need" and "there could have been a better response."
The lack of government response, he said, is prompting some people to organize themselves to help needy victims.
Gabriella Andreevska, who lives in southern Macedonia, said people from unaffected areas are planning to travel to flooded regions to help out.
She also said Macedonians are complaining the government hasn't responded well to the disaster.
Andreevska's said when a friend of hers called the authorities for help, she didn't get a response.
Instead she had to rely on a neighbor who came armed with a bucket to help her remove water from her flooded home.