The blaze occurred late Wednesday in the western city of Tetovo, where the facility was set up following a recent spike in infections in the region.
Health Ministry officials said injured medical staff and patients along with over evacuees were being transferred to hospitals in the capital Skopje, some 45 kilometers (28 miles) to the east, AP reported.
The cause of the fire was not immediately known, but Prime Minister Zoran Zaev said in a Facebook post that the blaze followed an explosion at the site.
It is so far unclear how many people were inside the hospital as the fire ignited. Neither it is known what has caused the fire, which reportedly raged for over an hour before being extinguished.
Tetovo, an Albanian-majority town of some 65,000 people, has reported a spike in Covid-19 cases, and currently has the second-highest number of infections in the country.
With less than 30% of the country’s population fully vaccinated, North Macedonia has seen a significant spike in infections and deaths since late August.