The problems at the NYSE began at 11:32 a.m. ET and resulted in the exchange halting trading in all stocks as it attempted to work on the issue.
The exchange didn't specify the nature of the problem beyond an "internal technical issue."
"NYSE has temporarily suspended trading in all symbols," the market said in a message to traders. "All open orders will be cancelled."
The stock exchange said it was not the result of a security breach.
That was echoed by White House spokesman Josh Earnest, who said that President Obama had been briefed by his Homeland Security Advisor, Lisa Monaco, who told him there was no sign that malicious actors were to blame.
The Securities and Exchange Commission said is was closely monitoring the situation and was in contact with the NYSE.
The disruption was the second of the day for the exchange.
Earlier in the trading session, connectivity to three of the NYSE's connection points for computerized trading were hit by a fault that caused trading in about 200 stocks to be halted.
Two of the affected gateways were returned to service and one was planned to be restored at the end of the Wednesday session.
Martyn Williams covers mobile telecoms, Silicon Valley and general technology breaking news for The IDG News Service. Follow Martyn on Twitter at @martyn_williams. Martyn's e-mail address is martyn_williams@idg.com