Charles Woodyard, the former CEO of the Chicago Housing Authority, left the agency amid sexual harassment allegations, WBEZ has learned.

On Oct. 15, Woodyard abruptly resigned after two years on the job. At the time CHA released a statement that quoted Woodyard as saying “I am pursuing other opportunities that I hope will benefit my family and my career.” Woodyard added he wanted to “spend more time guiding” his teenage son. But on Oct. 14, CHA signed a $99,000 settlement agreement with a former employee. WBEZ obtained the confidential agreement.

The female employee – whose name is redacted in records – alleges that she was a victim of sexual harassment, including physical contact by Woodyard. She alleges that she continues to require medical treatment for physical and emotional distress.

CHA and Woodyard deny the allegations.

“The allegations are false. I never sexually harassed anyone,” Woodyard told WBEZ.

The agreement says that one of the public housing agency’s reasons for settling is to avoid the expense and inconvenience of defending itself. The $99,000 includes back wages, attorneys’ fees and medical treatment for the former employee.

“The board took this allegation seriously, and determined it was in the best interest of the agency to settle it,” CHA board chair Z. Scott said in a statement.

In August, the female employee filed a charge of discrimination with the U.S. Equal Employment Opportunity Commission that said “during my employment, I was subject to sexual harassment. I complained to Respondent. Subsequently, I was disciplined and discharged. I believe that I have been discriminated against because of my sex, female, and in retaliation for engaging in protected activity.” She indicated that the latest discrimination took place in June.

Mayor Rahm Emanuel appointed Woodyard in 2011. Lewis Jordan, the previous CEO, was pushed out amid questions surrounding CHA credit card use. Woodyard had run the public housing authority in Charlotte, N.C. and has an extensive real estate background. His resignation from CHA took effect Nov. 1.

Beyond the sexual harassment allegations, there had also been concerns about how quickly Woodyard was getting things done. CHA is two years from supposedly finishing its massive original $1.6 billion Plan for Transformation, the blueprint for tearing down public housing and replacing some developments with mixed-income communities. CHA revealed Plan Forward, the second phase of the plan, this past spring. It focuses on acquiring homes in neighborhoods across the city for rehab and boosting economic activity around CHA sites.

The economy and fickle housing market have slowed down progress especially for selling market-rate units. Meanwhile, CHA promised it would rehabilitate or redevelop 25,000 units for public housing families. For fiscal year 2014, CHA plans to deliver 562 public housing units, but none of them will be on mixed-income sites. Originally, the Plan for Transformation was a five-year plan. Today, it’s supposed to be completed by 2015. That would mean the CHA would have to deliver a whopping 7,000 units by then.

Michael Merchant, former commissioner of the city Department of Buildings, is the new CEO.

Natalie Moore is a WBEZ reporter. Email: nmoore@wbez.org Follow Natalie on Google+, Twitter