The country's ATMs stopped working in the early afternoon and were down for an hour.
"It's a central fault," Johan Nilsson, spokesperson at Bankomat AB, told the TT news agency.
"It's deeply regrettable… we were only out of action for an hour or so but our goal, of course, it to always have cash available for our customers."
When the same thing happened late last month, Nilsson dismissed any notion of a hacker attack being behind the system's failure.
Thursday's incident likely went unnoticed among most Swedes, as only around a quarter of all retail transactions in Sweden involve cash.
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In August last year, Swedish company Bankomat revealed that it would take over all 2,220 of the country's automatic teller machines run by the five biggest banks. Bankomat is jointly owned by all five banks, Danske Bank, Handelsbanken, Nordea, SEB, and Swedbank.
The company promised at the time that transactions would run more smoothly than before.
Anyone affected has been urged to get in contact with Bankomat.