Johnson resigned over the weekend after inappropriate workplace communications were allegedly discovered, according to Lee's office.
Lee said in a statement Sunday that Johnson offered his resignation and she accepted, after an investigation into the communications was opened last week.
The San Francisco Chronicle reports those texts from 2024 were released last week as part of public records requests that were subpoenaed during a corruption investigation into recalled Mayor Sheng Thao.
Johnson could not be immediately reached Sunday to corroborate or refute Lee's characterization of the communications.
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"On Friday evening, I learned about certain degrading and unprofessional communications involving Mr. Johnson," Lee said in a statement. "We promptly conducted our own investigation and verified these communications, which are wholly incompatible with the values of this administration and those of the people of Oakland. Under my watch, I will not tolerate transgressions of this nature."
Lee appointed Assistant City Administrator Elizabeth "Betsy" Lake to take on the position on an interim basis. Lake has worked with the city of Oakland for the past 8 years and has 30 years of experience practicing law, according to Lee's office.
Johnson was appointed by then-Mayor Sheng Thao in 2023 for the position, which draws a yearly salary of $340,000. Johnson was city administrator for just under three years.
ABC7 Eyewitness News contributed to this report.