"I will know more ... in hours or days but according to our knowledge, five million Europeans have been affected out of those 50, which is an incredible number," she said.
Jourova said Facebook's quick revelation of the case demonstrated that new European rules on data protection implemented earlier this year are working.
New EU rules -- the General Data Protection Regulation (GDPR) -- have been billed as the biggest shake-up of privacy regulations since the birth of the web and give European regulators vast new enforcement powers.
The case for GDPR was boosted by another recent scandal over the harvesting of Facebook users' data by Cambridge Analytica, a US-British political research firm, for the 2016 US presidential election.