The day after Brussels gave the green light for a state rescue of Portuguese banking giant Banco Espirito Santo (BES), Juncker warned the recession-hit region remained vulnerable to fresh economic strains.
"I believe that we have gone a long way and we are nearing the end but we have not yet turned a corner," said Juncker during a visit to crisis-hit Greece, his first official visit to a member state since being elected as the head of the EU's executive arm.
Junker said the situation in Portugal remained "fragile," adding that "we must remain vigilant ... Across Europe, we could be affected by things which we cannot predict".
The crisis at BES has shaken confidence in Portugal, which has only just emerged from a three-year EU-backed aid plan, one of several countries to be rescued when they were frozen out of international debt markets.
After holding talks with Greek Prime Minister Antonis Samaras, Juncker emphasised that member states must continue with "fiscal discipline" despite the improving outlook in financial markets.