Gov. Gavin Newsom of California said Monday that the head of the state’s Department of Public Health resigned amid “personnel judgment questions” that contributed to the breakdown of the state’s disease reporting system.

Nearly 300,000 records, most of them from virus tests, disappeared from the system over the past two weeks, a problem that the state is currently rectifying.

“She wrote a resignation letter and I accepted her resignation,” Mr. Newsom said of the public heath director, Dr. Sonia Angell. “We are all accountable in our respective roles for what happens underneath us.”

In a letter to her colleagues at the California Department of Public Health, Dr. Angell on Sunday had cited “my own plans to depart from my position,” but did not give a specific reason for leaving.

The breakdown of the antiquated data system, which the governor on Monday vowed to replace, had clouded the overall picture of the virus’s progression in California, which as of Monday has had 10,378 deaths related to the virus, third in the nation after New York and New Jersey, and 567,908 confirmed cases, according to a database maintained by The New York Times.

On Monday Mr. Newsom said that despite testing delays and the problems with the disease reporting system that there were encouraging signs in the state’s fight against the virus. He cited a 19 percent decline in hospitalizations over the past two weeks. Last week the state had reported a 10 percent decline. Hospitalizations are counted using a separate system unaffected by the data problems.

Dr. Angell, who had been in her role for less than a year, was replaced by two people: Sandra Shewry, a veteran public health official, is now the acting director of the Department of Public Health, and Dr. Erica Pan, the former chief health officer of Alameda County, is now the acting state public health officer. In her role in Alameda County, Dr. Pan had clashed with Elon Musk, the billionaire entrepreneur and head of Tesla, over plans to reopen the company’s car factory in Fremont, Calif.