The airline's cards, which are used for earning frequent flyer points but can also act as credit cards, were frozen after it was found they had been used in Spain.
Several banks have in the past few weeks stopped cards used in the country.
Fraunke Plaß, spokeswoman for the Deutsche Kreditbank (DKB), which is Lufthansa's partner bank for the cards, said so far there were no known cases of fraud involving the Lufthansa cards.
The problem appears to relate to a particular billing company in Spain, which processes credit card transactions.
A spokesman for credit card firm Mastercard said there were reasonable grounds for suspecting the involvement of a company, rather than assuming it was individual cases of “skimming,” in which fraudsters use sophisticated card readers to collect credit card details from cash machines.
Visa and Mastercard recently warned banks that distribute credit cards that there were suspicions of widespread fraud relating to Spain. The British bank Barclays has also been affected.
Frank-Christian Pauli, a banking expert at the Federal Association of Consumer Groups, said there was a “criminal industry” that collected credit card data and used it for fraudulent transactions.
“We can't protect ourselves against it,” he said.