Video report by ITV News Europe Editor James Mates
It is warning its 27 nations to move cautiously as they return to normal life, and to base their actions on the scientific advice.
People have died in Europe after contracting Covid-19.
With Denmark, Austria and the Czech Republic already lifting some lockdown measures, the European Commission rushed out its road map for members of the world’s biggest trade bloc to co-ordinate an exit from the lockdowns.
It comes as children up to the age of 11 are returning to nurseries and schools in Denmark, as the government becomes the first in Europe to relax coronavirus restrictions on education.
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Denmark's Prime Minister Mette Frederiksen welcomed children as they went back to school in the capital Copenhagen.
Denmark was among the first countries in Europe to impose a lockdown, with schools closed on 12 March.
Meanwhile, Germany plans to let smaller shops reopen next week after the coronavirus shutdown, and to start reopening schools in early May.
But Europe’s biggest economy is keeping strict social distancing rules in place for now.
“We are moving forward in small steps and must see what effect they have,” Ms Merkel said.
The EU commission expects a return to normality should take at least a few months and involve large-scale testing.
About 80,000 people have died in Europe from Covid-19 - two-thirds of the global toll - according to the European Centre for Disease Prevention and Control.
The commission said those scientists should be relied upon to guide national exit strategies in the weeks and months to come.
The EU is split in its approach - France this week renewed its lockdown until May 11, and Belgium appears to be heading in a similar direction, while Spain recently renewed its state of emergency for the second time for an additional two weeks.
“This is not - it is not - a signal that confinement, containment measures can be lifted as of now,” European Commission president Ursula von der Leyen told reporters, highlighting the need for clear communication across the bloc as countries emerge from quarantine.
Warning that lifting restrictions will "unavoidably lead to a corresponding increase in new cases", the commission said this should only start when the spread of the disease has dropped significantly and for some time, and when hospitals can cope with more patients.
While the commission, which proposes EU laws and ensures they are enforced, does not spell out exactly how EU countries should make the transition, the road map does underline that "action should be gradual".
"A lack of co-ordination in lifting restrictive measures risks having negative effects for all member states and creating political friction," the document said.
Business operations should be phased in by sectors, based on things like how much can be done over the internet, the economic importance of the industry, or the kinds of shift work that could be introduced.
Social distancing should be maintained and there should be no general return to work, it says.
Shops could gradually reopen, with possible limits on the number of people who could enter, and school could start again, although the commission recommends smaller classes to allow pupils to work at a safer distance from each other.
Lunch breaks could be set at different times and internet learning should be preferred where possible.
Brussels also said a gap of around one month should be left between any steps to monitor their impact.
Elderly people should be protected for longer, while restaurants, bars and cinemas could resume business with restricted opening hours and limits on the number of people who could enter.
Measures blocking mass gatherings like festivals and concerts would be among the last to be lifted.
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