"While the evolution of the pandemic is getting back to March levels, our state of preparedness is not," the EU executive's vice-president Margaritis Schinas said.
He urged EU states to adopt a common strategy for the new phase of the pandemic and avoid the "cacophony" of different national measures that characterized the first months on the pandemic on the continent.
With new cases hitting about 100,000 daily, Europe has by a wide margin overtaken the United States, where more than 51,000 COVID-19 infections are reported on average every day.
As trials of COVID-19 vaccines advance, with the first shots potentially available by the end of the year according to the World Health Organization, Brussels is urging EU governments to prepare vaccination plans.
Health policy is a national prerogative in the 27-country bloc and the EU Commission can only make recommendations for common measures.
Hospitals and vaccination services should be properly staffed with skilled workers equipped with necessary protective gear, the Commission said, urging governments to avoid the shortages that dogged the bloc when the epidemic flared up in March.
Vaccines should be made available first to the most vulnerable groups, which include healthcare and long-term care facility workers, people over 60, people with chronic diseases, essential workers, and more disadvantaged socio-economic groups.
According to a conservative estimate, made by the Commission in July, people belonging to "priority groups" could be over 200 million of the EU population of 450 million.
The Commission also called on EU governments to prepare for the possible distribution of vaccines that may need to be stored at extremely low temperatures.
(Reporting by Francesco Guarascio @fraguarascio, editing by Robin Emmott)