In a statement, it flagged Aragon, Catalonia – which includes Barcelona, and Navarra due to their “high infection numbers and local lockdowns.”
The regions have seen a huge rise in cases during recent days, but Spanish authorities insist that infections in most regions are under control.
It comes as Germany’s Robert Koch Institute (RKI) said negligence was to blame for a recent rise in cases around the country.
“The new developments in Germany make me very worried,” RKI head Lothar Wieler told reporters.
The number of new cases in Germany almost doubled on Tuesday to 633, and the RKI has blamed the increase on social contact in workplaces.
A spike in the infection rate in the northern regions of Catalonia (63.1 per 100,000 inhabitants), Aragón (160.1 per 100,000) and Navarre (79.2 per 100,000) have pushed Spain’s average up to 39.4 per 100,000 inhabitants, far higher than Germany’s infection rate of 7.7 (data from European Centre for Disease Prevention and Control).
The travel advice by the German government follows the UK’s sudden decision on Saturday to impose a 14-day quarantine on British holidaymakers returning from Spain.