The Black Employees Alliance and Coalition Against Anti-Blackness filed the complaint Monday with the California Department of Fair Employment and Housing and alerted the city’s Ethics Commission. The group also laid out its grievances, based on city data from 2012 to 2020 obtained via public records, in a letter to Mayor London Breed, the Board of Supervisors and department heads that said “San Francisco should be ashamed.”

“It’s an injustice,” said Jessica Brown, a Black manager with the city who is on the Black Employees Alliance’s leadership team. “We really want the city to move into action.”

The city disputed the claims about disparities in raises in the group’s complaint, citing pay data, but has acknowledged racial gaps in discipline and pay in the past that San Francisco is addressing.

“The Department of Human Resources takes any claim of discrimination or unfair treatment of any employee very seriously,” spokesman Mawuli Tugbenyoh said in a statement. “We have implemented focused strategies to address any inequities that we have on many occasions openly discussed and reported on.”

The state will meet with the Alliance in May to determine whether to accept the complaint for investigation.

Black people make up 12% of the city’s 36,000-strong workforce. The Black Employee Alliance consists of around 410 members. The group’s state complaint follows a trio of racial discrimination lawsuits against the city and a human resources scandal last year over a forged discrimination settlement. The city has admitted racial disparities and founded an Office of Racial Equity, requiring each department to produce a racial equity action plan and taking steps to reduce bias in five main areas of hiring and work practices.

“We have a lot of work to do, but it is very valid that Black employees are paid less in certain roles, are not promoted proportionally and that they are the subject of disproportionate disciplinary actions by city departments,” Board of Supervisors President Shamann Walton said in a statement, reacting to the state complaint. “This has to change.”

Andy Lynch, a spokesman for the mayor, said she has met with the Black Employees Alliance in the past and is always willing to listen and work with city employees who feel they are not treated fairly.

“The city takes all claims of discrimination seriously,” Lynch said.

The Alliance’s complaint highlighted city data that showed Black employees are disproportionately disciplined. Last fiscal year, Black employees were the subject of 21% of corrective actions and disciplines, although they make up only 12% of the workforce. Numbers had improved from the previous fiscal year.

“This is still unacceptable to the department, but is a step in the right direction,” Tugbenyoh said.

The city improved training, increased awareness and publicized data about disparities, he said, and is finalizing guidance and training on disciplinary processes to make sure they’re equitable across departments.

Dante King, a leader with the Black Employees Alliance, said the problem persisted and the city hasn’t done enough to fix it. He referred to a two-page outline with questions managers should ask when meting out discipline as insufficient guidance and accountability.

“That does not go far enough,” he said.

The Alliance’s complaint also alleged pay and bonus disparities between white and Asian versus Black managers based on a small sampling of data.

Managers who are at the top of their salary level can nominate themselves for annual raises. They can also get wage increases throughout the year for a number of reasons, including promotions and job reclassification.

“San Francisco has been allowed to show favor to who they want to,” said Irella Blackwood, a board member of the Municipal Executives Association and a Black manager who has worked for the city for 10 years.

The city pointed out that data shows last fiscal year, Black managers, who made up 11.26% of the payroll, received 12.08% of annual raises. Asian managers, who are 17.61% of payroll, received 18.72%. White managers, who were 54.72% of the payroll, received 52.28%.

Managers of each race received around 17% of wage increases outside of annual bonuses in the past five years.

The complaint also took issue with the budget for annual raises for white managers that swelled to over $1 million last fiscal year. The city provided data that showed that while the budget for white manager bonuses increased by 51% over the past five years, the amount for Black managers increased by 65% during the same time period.

“The City does not vary how it pays its employees by race for performing the same work,” Tugbenyoh said. “To the extent that pay varies by race, it is because of the jobs people are employed in.”

Despite disputes over disparities in raises, the city has admitted in the past to racial pay gaps. A report last March documented that Black employees held lower-paying jobs, were less likely to be promoted and were more frequently disciplined and fired.

In response, the city launched a diversity recruitment team, removed some information about job applicants to try to limit implicit biases in the interview process, expanded trainings in departments and posted workforce demographic data on its website. The city also hired an independent consultant to examine its Equal Employment Opportunity complaint process.

The Board of Supervisors is waiting for a report from the Mayor’s Office before holding a hearing, Walton said. The result could be possible legislation and a charter amendment to change practices and try to eliminate bias in how complaints are evaluated and ignored.

Chronicle staff writer Jessica Flores contributed to this report.

Mallory Moench and Jessica Flores are San Francisco Chronicle staff writers. Email: mallory.moench@sfchronicle.com, jessica.flores@sfchronicle.com Twitter: @mallorymoench, @jesssmflores