A police statement said that on arriving in response early yesterday to the disturbance, "officers were confronted by a combative subject resulting in the discharging of the officer's weapon, fatally wounding two individuals."
The killings are the first in the city since protests last month over a video showing a white police officer in Chicago shooting 16 times at a fleeing black teen, who died at the scene.
The shooting, which took place in 2014, has triggered a federal civil rights probe into the police.
Updating the statement later, police said: "the 55-year-old female victim was accidentally struck and tragically killed. The department extends its deepest condolences to the victim's family and friends."
There was no information on the identity of the police officers.
LeGrier struggled with mental health issues and was threatening his father with a baseball bat, relatives told the Chicago Tribune.
Police were summoned and the father asked Jones, a neighbor, to look out for the officers.
"His father was scared because that's not his character," LeGrier's mother Janet Cooksey, who was not present, told the Tribune.
Police referred all questions to the Independent Police Review Authority, the agency that investigates possible police misconduct.
Police tactics and racism have been the subject of a national debate since protests erupted in Ferguson, Missouri, in mid-2014 over the shooting death of black teenager, 18-year-old Michael Brown.
Chicago's Laquan McDonald, 17, was gunned down just a few months later but the case was ignored until a court in November ordered the release of a police dashcam video that captured the shooting.
"Our objectives are to conduct thorough and timely investigations of each incident," Fairley said. She gave no further information.
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