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 under-reported 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.
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Still, officials believe the COVID-19 trends reported by Gov. Gavin Newsom and others over the past few weeks remain consistent.
Newsom has ordered a full investigation of the issue, Ghaly said.
"We will hold people accountable," he added.
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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.
"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 said Friday that no counties have been removed -- or added -- since last Friday. That's because the state froze the watch list in order to make sure its data was accurate.