"We do not see any indication of a cyber breach or a cyber attack," FBI Director James Comey told the Senate Intelligence committee.
New York Stock Exchange resumed trading at 3:10 p.m. Eastern after an outage of nearly four hours.
The New York Stock Exchange stopped trading late morning Wednesday because of a technical problem, though NYSE-listed shares continued to trade on other exchanges.
The exchange said on its official Twitter feed that the issue was internal and not related to a breach of its systems.
(1 of 3) The issue we are experiencing is an internal technical issue and is not the result of a cyber breach.— NYSE (@NYSE) July 8, 2015
(2 of 3) We chose to suspend trading on NYSE to avoid problems arising from our technical issue.— NYSE (@NYSE) July 8, 2015
(3 of 3) NYSE-listed securities continue to trade unaffected on other market centers.— NYSE (@NYSE) July 8, 2015
Trading came to a halt two hours after it was discovered some stock orders were not being processed. Early on, the problem appeared to be related to an overnight software upgrade. The decision to halt trading was intended to prevent some to be helped and others to be hurt as the all-electronic system was malfunctioning.
"In the interest of fairness, people who are closer to it may have an advantage, so rather than worry about that they just shut everything down so it's equal, if you will," Raymond James Vice President David Lucas said.
The suspension of trading went past two hours and the system was finally fixed after nearly four hours.
The halt came on a day when markets around the world are continuing to worry about the debt crisis in Greece and a major sell-off in Chinese stock markets.
However, it's not likely the average investor got hurt Wednesday, according to Santa Clara University finance and investment professor Robert Hendershott. "Most people are probably not even aware of the trading halt. They're certainly not trying to trade. The only situation would be if you're closing on a house and you had to sell some stocks today it would be a real problem, but that's not for very many people," he said.
Federal regulators and the White House monitored the unusual suspension, but took no action after being assured by National Security Advisor Lisa Monaco this was not a cyber attack. "Miss Monaco told the president that at this point there's no indication that malicious actors are involved in these technology issues," White House Press Secretary Josh Earnest said.
Still, what happened on Wall Street is a wake-up call. "For the average public, it starts to sound, it makes me nervous like something isn't working, so I am concerned," Howard Lyons said.
The Dow Jones industrial average lost 261 points, or 1.5 percent, to 17,515. The Standard & Poor's 500 gave up 34 points, or 1.7 percent, at 2,046 and the Nasdaq was down 87 points, or 1.8 percent, at 4,909.
SEC Chair White: “We are in contact with NYSE and closely monitoring the situation”— SEC_News (@SEC_News) July 8, 2015
U.S. markets have experienced other technical problems in the past as more trading is handled by computers, illustrating the fragility of the infrastructure that financial markets use.
In May 2010, the Dow Jones industrial average plunged hundreds of points in minutes in an incident that later became known as the "flash crash." In March 2012, BATS Global Markets, a Kansas company that offers stock trading services, canceled its own IPO after several technical snafus.
Two months later, a highly anticipated IPO of Facebook on the Nasdaq exchange was marred by a series of technical problems, rattling investors unsure if their orders to trade went through.
Stock in the company that owns the New York Stock Exchange is trading despite the halt on the floor, and it is falling. The IntercontinentalExchange Group, which bought NYSE Euronext in late 2012, fell $3.47, or 1.5 percent, to $223.71. That compares with a drop of 1.1 percent for Standard and Poor's 500 index. The stock of the Nasdaq OMX Group, the company that owns the rival Nasdaq market, fell 83 cents, or 1.7 percent, to $48.03.
The Associated Press contributed to this story.