The NYPD sergeant who fatally shot a mentally ill Bronx woman in her home was charged with murder on Wednesday afternoon, pleading not guilty and posting a $100,000 bond. Sgt Hugh Barry was also charged with manslaughter and criminally negligent homicide for the shooting that sparked protest and deeply troubled top NYC officials.

Barry shot Deborah Danner in October after police were called to her apartment by a neighbor for a disturbance. Danner, a 66-year-old black woman with schizophrenia, had allegedly approached the officer with a bat after briefly wielding a pair of scissors.

Bronx borough president Ruben Diaz said in a statement Wednesday that the decision was “a positive first step towards addressing an issue that has been long neglected”.

“Clearly, there were options available to Sgt Barry which he failed to implement, and his conduct in this case is by no means a reflection on the great work of the New York City Police Department and its dedicated members,” he added.

Both the city police chief and the mayor, Bill de Blasio, also condemned the shooting in its immediate aftermath. Barry has been placed on modified duty, and was stripped of his gun and badge while the incident was investigated by the department’s force investigation division.

“What is clear in this one instance: we failed,” the police chief, James O’Neill, told reporters as details began to emerge in the case. “That’s not how it’s supposed to go. It’s not how we train.”

De Blasio added: “The shooting of Deborah Danner is tragic and it is unacceptable ... This should never have happened. It’s as simple as that. Deborah Danner should be alive right now. Period.”

Danner had penned an incisive essay on her fears of being killed by police due to her mental illness about five years before she died, it was discovered after her death.

“We are all aware of the all too frequent news stories about the mentally ill who come up against law enforcement instead of mental health professionals and end up dead,” she wrote, as she called for better training for the police to deal with individuals experiencing mental health episodes.

In her appeal, she referenced Elaine Bumpurs, a Bronx woman killed in 1984 after waving a knife at officers during an eviction. Danner, it turned out, would meet the same fate in the same borough, at the same age as Bumpurs – both were 66 – 32 years later.

Sergeants Benevolent Association president Ed Mullins called the decision “an absolute disgrace” in a statement. The association has publicly sided with Barry and against O’Neill to date, arguing that the officer was reasonably fearful for his life when he fired his weapon.