"If we do not spend the winter break at home, then unfortunately we will increase the likelihood of a so-called third wave, which is already being talked about in Europe,” Niedzielski said.
A third wave of the coronavirus would coincide with the peak of the flu season in February, he added.
The winter school holidays in Poland are when many families usually head off for ski trips.
Deputy Prime Minister Jarosław Gowin said on Tuesday that ski slopes in Poland would be allowed to open this winter, with safety protocols in place.
However, hotels, B&Bs and restaurants in Poland will remain closed.
The two-week school winter break starts on January 4 across the country. In previous years, the holidays took place on different dates in different parts of Poland.
Meanwhile, the government plans to allow five people at most, excluding family members living together, to take part in traditional meals in their homes on December 24.
Poland on Wednesday reported 15,362 fresh COVID-19 infections and a record 674 new deaths linked to the coronavirus.