After JPMorgan Chase & Co.'s website went down Wednesday for the second time this week, the company said it would refund late fees and help fix other outage-related problems for the 16.6 million online customers who were unable to access their accounts.

"We will work with customers on any issues that occurred, including late fees," Tom Kelly, a spokesman for JPMorgan Chase, said by e-mail Wednesday.

The site went down late Monday night and service was restored around 1 a.m. New York time Wednesday. The system failed again several hours later, though it appeared to up and running at midday.

The problem was a software glitch and customers' accounts were not at risk, Christine Holevas, a company spokeswoman, said in an interview. Customers trying to use the site saw an error message that read, "Our website is temporarily unavailable. We're working quickly to restore access."

The length of the outage raises operational risk and internal control issues for the bank, said Christopher Whalen, a former analyst for the Federal Reserve Bank of New York and co-founder of Institutional Risk Analytics in Torrance, Calif.

"These systems are big and complex, but they should have redundancy to take the 'A' system offline if need be for hours at least," Whalen said.

Subscribe Now

Access to authoritative analysis and perspective and our data-driven report series.

14-Day Free Trial

No credit card required. Complete access to articles, breaking news and industry data.