Officials were quick to say that every call was answered and emergency workers continued to be dispatched across the city.
However, the problem - which officials said halted the relaying of electronic messages between 911 operators and the dispatchers who send out police, fire and emergency workers - continued Thursday on the first truly hot day of the year, when there is usually a spike in calls.
As a result, calls were being prioritized to ensure that the most serious cases were dealt with first, according to fire officials.
Police Commissioner Raymond W. Kelly, whose department is responsible for oversight of the 911 system, said that every call that came in had been answered.
On Wednesday, the system went down for 16 minutes. Operators were forced to fill out slips describing an emergency, Kelly said, and then use "runners" to send those notes to the dispatchers who work on the same floor in the 911 headquarters in Brooklyn.
Officials believed they had corrected the problem, but the computers went dark for a second time early Thursday, this time for six minutes, Kelly told reporters later in the day.
"They thought they had it fixed at 3 a.m. this morning and then obviously this happened again, so it's being thoroughly examined," he said.
Shortly after Kelly made his remarks, the system went dark for around 15 minutes a little after noon.
The problems occurred as the city continues to work to modernize and improve its 911 system, a $2 billion project meant to upgrade a system that has failed in the past, often when needed most.
Most notably, it failed on the morning of the Sept. 11 attacks, when an older system was overwhelmed by the volume of calls.
During a 2010 blizzard, as the city was preparing to install parts of the new system, it was overwhelmed again. A review by an outside consulting firm found persistent problems, and the Bloomberg administration vowed to address the concerns.
Last year John C. Liu, the city comptroller, released an audit that was scathing in its criticism of the administration, saying it had both mismanaged and overpaid for the 911 upgrade. Now a candidate for mayor, Liu issued a statement Thursday affirming his concerns, saying that was troubled that the city needed to rely on an outside consultant to maintain a functioning 911 system.
The problem, he said, shows "the need to make sure our safety isn't held hostage to troubled technology that can only be maintained by an outside consultant."
John J. McCarthy, a spokesman for Mayor Michael R. Bloomberg, said the problems were not reflective of a broader issue with the changes being made to improve the system.
Rather, he said, the errors occurred as workers continue to switch to the newer system. As part of the change, they must reboot their computers. The reboot has caused the system to go down for brief periods, during which operators resort to the old-fashioned pen and paper system.
City officials say they expect the upgrade to be complete by 2015.
The updates being made are with the dispatch system, said Bruce Gaskey, the director of the Mayor's Office of Citywide Emergency Communications. The current system is 40 years old and has long needed improvements, he said.
"They are getting much more functionality out of this, and as you do in any cutover, you have to work out the kinks," Gaskey said.
He said the public would not be affected as problems were addressed.
(J. David Goodman contributed reporting.)