A computer malfunction that forced the New York Stock Exchange to suspend trading for more than three hours on Wednesday was caused by an update to part of the exchange's trading software before markets opened.

The update threw off the entire system.

The NYSE reopened at 3:10 p.m. ET the same day, after being halted shortly after 11:30 a.m. During the shutdown, NYSE said the outage was due to an internal technical issue and not the result of a cyberattack. Other exchanges were trading normally throughout.

On Thursday, the exchange elaborated on that explanation, saying an update to the software the exchange uses to properly determine timestamps on trades was improperly rolled out.

After installing new software before markets opened Thursday, the exchange began hearing about connectivity issues between customers and the trading units that had been upgraded.

"It was determined that the NYSE … customer gateways were not loaded with the proper configuration compatible with the new release," once markets opened, the exchange said, which caused them to shut down the whole market and cancel all outstanding orders.

During the three-hour outage, trading in U.S. stocks continued on 11 other lesser-known stock exchanges across America.  The TSX also remained open, losing about 200 points on Wednesday.