With nearly 30 million online banking customers and the nation’s busiest bank Web site, the failures spurred consumer anger, with account holders in some cases unable to pay bills electronically or check their balances.

“Our priority is delivering the speed and functionality our customers expect,” said David Owen, senior vice president and head of online and mobile banking for Bank of America. “We take this very seriously, and this has been very disappointing in terms of not meeting those expectations this week.”

While the site seemed to be functioning normally by Wednesday evening, Mr. Owen was not declaring victory. “We’re taking this day by day,” he said.

The problems first cropped up on Friday, a day after the bank, the nation’s largest, announced it would impose a new $5 a month charge for some debit cardholders. But Mr. Owen insisted the problems were not caused by hackers unhappy with the new fee or by efforts to flood the site with traffic as a protest, a strategy called a denial-of-service attack.

“Everything we know does not point to third-party intervention,” he said. Along with hundreds of internal analysts and technical staff, Mr. Owen said the bank had also been consulting with federal law enforcement officials and outside industry experts to get to the root of the Web troubles.

The problems were at their worst on Friday — the day after the $5 fee was announced — but Mr. Owen pointed to other causes like weekly paydays and federal government disbursements at the beginning of the month for the increase in visitors to the site.

“It’s a series of events that have converged,” Mr. Owen said. Besides the increased traffic, Mr. Owen said the company was in the middle of an effort to replace an old computer system while also offering customers new options when they used the site. The combination of factors made the problem more time-consuming to fix.

As the company identified and fixed individual bottlenecks, he said, other problems would spring up elsewhere, delaying the effort to get the Web site working normally again. “Sometimes, it’s as simple as fixing a box or changing a setting. But that’s not the case in this instance.”

The Bank of America Web site had 24.3 million unique visitors in August, according to data compiled by comScore, several million more than rivals like JPMorgan Chase, Wells Fargo and Capital One.

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