Margaritis Schinas' comments come after Estonia, Latvia and Lithuania opened their internal borders to each other last week in a bid to give their economies a timely boost.
The EU Commission has warned against continuing mini-Schengen areas after Europe's COVID-19 pandemic has eased.
Estonia, Latvia and Lithuania opened their internal borders to each other last week in a bid to give their economies a timely boost.
They were able to lift border controls ahead of many other European countries because of relatively low infection rates.
But Margaritis Schinas, vice president of the European Commission, said he didn't want the so-called 'Baltic bubble' to be a long-term feature.
He said the current restrictions should not be "replaced by some sort of regional mini-Schengens that fragment our Single Market".
"This is not possible," he told Euronews. "On the contrary, it is possible, as recommended by the commission, that regions and member states that have similar epidemiological records can indeed use this intermediary phase to start lifting internal border restrictions in an orderly and non-discriminatory way and, above all, a safe way for travellers and tourists."
The lifting of border controls is set to play a key role in salvaging Europe's summer tourism season and provide vital income for hotels, bars and restaurants.
Spanish academics have suggested dividing the continent into green and red areas, based on how hard hit they have been by COVID-19. Their idea would be to let tourists only travel between green areas, a proposal that does not seem to chime with Schinas' thinking.
Emergency COVID-19 legislation
Speaking on Euronews' Global Conversation, Schinas also touched on the issue of special powers being handed to some European governments to fight the COVID-19 pandemic.
There has been a particular focus on Hungary after MPs granted Prime Minister Viktor Orban powers without a time frame.
Schinas this kind of legislation should be "grounded in the rule of law" and "fully compatible with European values and principles".
He also suggested Orban is considering giving up those powers soon and praised the EU's "pressure and scrutiny" in bringing this about.