Not all of the records are coronavirus test samples, but most of them are, Ghaly said. The group of records may also include some duplicates, which the state is currently working to sort through and eliminate.
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The issue has been fixed, but working through the backlog is expected to take 24 to 48 hours, he said.
State officials believe the number of new COVID-19 cases in California has been underreported since July 25, when a server outage created a delay in lab records coming into the state's reporting system. At the same time, the state hadn't realized they weren't receiving data from one of the largest commercial labs for five days. Those problems combined have created the extensive backlog.
"Our data system failed and that failure led to inaccurate case numbers and case positivity rates. It also prevented counties from having some of the data they need to monitor and respond to the virus in their communities," said Dr. Ghaly.
VIDEO: California health secretary Dr. Mark Ghaly addresses COVID-19 data glitch
Still, officials believe the COVID-19 trends reported by Gov. Gavin Newsom and others over the past few weeks remain consistent. Ghaly also said no changes to California's response policies were based on the incomplete data.
Gov. Newsom has ordered a full investigation of the issue, Ghaly said.
"We will hold people accountable," he added. "You deserve better, the governor demands better of us and we are committed to doing better."
Local health officers have expressed frustration with the data glitch, saying it's hard to address the COVID-19 crisis without knowing its true impact at the moment.
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In an emailed statement to ABC7 News, Contra Costa Health Services wrote: "We have had to stop calculating our positivity rate because positive results come back faster and were likely making our rate look artificially high."
Contra Costa said delays also hurt contact tracing efforts.
"We just don't know. We don't know if our cases are rising, plateauing or decreasing," said Santa Clara County Health Officer Dr. Sara Cody. "It's not just inconvenient, but this lack of data doesn't allow us to know where the epidemic is heading, how fast it's growing or not."
Another source of frustration for many counties has been how to get off the state's COVID-19 watch list, which needs to happen before districts are allowed to reopen schools. Ghaly revealed Friday that no counties have been taken off - or added on - since last Friday. That's because the state froze the watch list in order to make sure its data was accurate.
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"It's not inaccurate. What we're getting is correct, but we're not getting all of it," Santa Clara County COVID-19 Testing Officer, Dr. Marty Fenstersheib told reporters on Friday.
"We operate no matter what," he continued. "So, we will eventually get the right data."
Solano County Public Health Officer Dr. Bela Matyas said his office noticed the difference in numbers on July 23. They immediately alerted the state.
"It wasn't the first time we've had this issue. This issue has been going off and on, a day here a day there, really for over well over a month," Dr. Matyas explained. "But it became particularly pronounced on to us on July 23."
He said the state started working on the issue immediately. Matyas acknowledged, "it's a really tricky situation to solve, apparently."
"It wasn't built for this type of volume and for this type of a purpose," he said about the system. "And so it's being taxed very heavily. Not surprising that it's going to have some glitches... and that's sort of what we're experiencing right now."
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Additionally, Dr. Matyas said, "Keep in mind that the reason these numbers are so important is because we're trying to contain the disease. But this disease isn't containable."
"So an argument could be made that it really doesn't matter whether we get these cases, timely or not," he continued. "It's not going to change what we can do about the outbreak. The best we can do is mitigate harm, not stop the spread."
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Still, Matyas admitted that at its core, the massive delay presents a greater health issue.
"By the time we're talking to an individual who has a case, it's way too late to isolate them," he said. "We can learn about their contacts, but it's way too late to quarantine them- too much time has passed."
For months, state leaders have maintained that reopening decisions would be made based on science and data.
"We apologize. You deserve better, the governor demands better of us, and we are committed to doing better," Dr. Ghaly shared.
He said the state is making changes, including developing a new laboratory reporting system for COVID-19.
WATCH LIST: 38 California counties where COVID-19 is getting worse
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