A computer malfunction shut down Japan Net Bank's online deals for 22 hours through Friday afternoon, the company said.
The Internet-only bank said the problem occurred at 6:14 p.m. Thursday in the bank's database server, which manages customer accounts, including savings and transfers.
As an emergency measure, Japan Net, a unit of Sumitomo Mitsui Banking Corp., allowed its customers to make deposits and withdraw up to 100,000 yen at Sumitomo Mitsui bank branches and offices.
The computer problem rendered unavailable all of Japan Net's services, including transfers via its Web site as well as making transactions at its business partners' automated teller machines.
Many of the firm's roughly 670,000 depositors use the online settlement service for Internet shopping or auctions.
The firm said it fixed the problem shortly after 4 p.m.
The latest trouble follows trading difficulties April 28 and April 30, which prompted the online bank to add network communications circuits during the May 3-5 holidays.
Japan Net, which became operational in October 2000, is Japan's first Internet-only bank. Its trading system was disrupted for half a day in January 2002 due to a computer failure.