Jason Szenes/European Pressphoto Agency

The United States stock market showed again on Thursday that it remained vulnerable to technological breakdowns even as regulators and market operators work to keep up with trading that is increasingly electronic and driven by speed.

The latest trouble shut down trading on the Nasdaq market and its more than 3,000 stocks — including some of the most popular among investors, like Apple and Google — for more than three hours Thursday afternoon.

The disruption on the nation’s second-largest stock market, after the New York Stock Exchange, reverberated up and down Wall Street, affecting other markets as investors cautiously stepped back. Brokers scrambling to trade elsewhere discovered that they could not complete trades while in the dark about prices on Nasdaq.

“It is everybody — nobody can trade,” Manoj Narang, the chief executive of Tradeworx, said during the afternoon. “I’ve never seen anything like this.”

Some expressed relief that the problems came in August, typically a slow time for Wall Street.

“We didn’t lose any money on the shutdown, but we also made very little money today,” said the chief executive of one Wall Street firm, who asked not to be named.

Nasdaq officials said the halt was prompted by a problem with the data system that disseminates prices and that its cause had been “identified and addressed.”

The breakdown came just two days after Goldman Sachs accidentally sent out a barrage of errant trades that disrupted the exchanges where options are bought and sold. The two episodes have amplified questions about the reliability and integrity of financial markets that companies depend on to raise money and Americans trust with their retirement savings.

More than a year ago, the eagerly awaited market debut of Facebook shares was marred by a delay and technical problems. In May 2010, computer malfunctions were blamed for the “flash crash” when a flurry of stocks plunged to $1 or less and the Dow Jones industrial average plummeted more than 700 points in a matter of minutes.

While regulators and market participants have taken several steps to strengthen their systems, the problems this week suggest that the flaws in the markets have not been repaired, and may actually be getting worse.

“You have a very Rube Goldberg system,” said Gene Noser, co-founder of the brokerage firm Abel/Noser. “We’ve just put patches on it without attacking the basic problems.”

The persistence of technical flaws — each seemingly coming from a different part of the system — has been blamed on the complexity of the trading technology and the fragmentation of the market itself. In contrast to the days when the New York Stock Exchange competed only with the Nasdaq, today there are 13 public exchanges competing in a fast-changing and low-margin business.

The frustrations over the breakdowns represent an immediate challenge for the regulatory agency that oversees the stock markets, the Securities and Exchange Commission, and its new chairwoman, Mary Jo White.

Thursday evening, Ms. White said in a statement that the paralysis at the Nasdaq was “serious and should reinforce our collective commitment to addressing technological vulnerabilities of exchanges and other market participants.”

She said she would push ahead with recently proposed rules that would add testing requirements and safeguards for trading software. So far, those rules have faced resistance from the exchange companies. Ms. White said that she would “shortly convene a meeting of the leaders of the exchanges and other major market participants to accelerate ongoing efforts to further strengthen our markets.”

Despite the turmoil, stock prices ended largely unscathed on Thursday. The Nasdaq composite index rose slightly after trading resumed about 3:30 p.m. and finished the day up 1.1 percent. For much of the afternoon, the index was moving in a flat line across computer screens because none of the stocks in the index were trading.

In addition, the Dow climbed 66 points, or 0.4 percent, to close at 14,963.74. And the Standard & Poor’s 500-stock index rose 14 points, or 0.9 percent, to 1,656.96.

In the bond market, interest rates were unchanged with the yield on the 10-year Treasury note remaining at 2.89, and the price of the benchmark 10-year Treasury note was the same as late on Wednesday, at 96 20/32. But many industry participants said it would take time to quantify the losses from the incident. For banks, the unexpected inability to trade particular stocks disrupted complicated trading strategies that rely on being able to buy and sell quickly in several markets at the same time.

Broker dealers lost the revenue from the trading that should have been occurring. The volume of trading in stocks listed on the Nasdaq exchange fell 34 percent, or $16 billion, from where it had been the previous day.

Nasdaq was already facing skepticism in the industry over its handling of the Facebook initial public offering, which was botched because of a flaw in a different part of Nasdaq’s computer systems.

The market operator paid a $10 million fine for its mishandling of the initial public offering, but a number of banks felt they were never fairly compensated for the losses they suffered as a result of the market operator’s error.

A number of industry participants were also unhappy with the way that Nasdaq executives, including the chief executive, Robert Greifeld, withdrew from the public eye immediately after the problem, providing few explanations of what happened.

Arthur Levitt, the former chairman of the Securities and Exchange Commission, said that Nasdaq was making the same mistakes after Thursday’s trading halt, when Mr. Greifeld and other Nasdaq executives again refrained from publicly commenting on the mishap.

“The worst part of all of this is the lack of disclosure — the lack of transparency,” Mr. Levitt said. “This is inexcusable.”

Nasdaq first sent out an alert at 12:14 p.m., telling traders that it was halting trading in all stocks listed on the exchange until further notice. The market operator said at that point that the issue was a result of problems with the system on which trades are recorded. Trading was also halted on all Nasdaq options markets.

Under normal conditions, if an exchange has problems, traders can direct their orders to other public exchanges. But because the problems involved the data feed from which prices are derived, all exchanges stopped trading Nasdaq stocks on Thursday.

During the halt, trading firms across Wall Street struggled to determine what to do with orders for Nasdaq-listed stocks.

“There is no transparency for investors at this point,” said David Warhoftig, managing director of Highside Capital Management, during the halt. “We were able to potentially get a few trades done when this first started, but now we are not able to do anything.”

Soon after the problems began, Nasdaq executives joined an open phone call with other exchanges and regulators in which they talked through the problems. Mr. Greifeld spoke separately on the phone with Ms. White, the S.E.C. chief.

But traders complained that Nasdaq provided few details on what had happened and how the problems would be resolved.

Jonathan Corpina, a stock trader at Meridian Equity Partners on the floor of the New York Stock Exchange, said that he had many clients calling him “looking for answers and explanations because they can’t get through to the Nasdaq on the phone.”

Shortly after 2 p.m., Nasdaq said in an alert that trading would begin again at 2:45 p.m., but that was pushed back and activity fully resumed only shortly before the trading day drew to a close at 4 p.m.

One of the stocks that could not trade on Thursday afternoon was Nasdaq’s parent company, Nasdaq OMX. When its shares reopened for trading, they slumped, closing down 3.42 percent.