"I know there are better ways to do this," said Circuit Attorney Kim Gardner.
At a news conference Friday, Gardner said she respected the judge's decision, but was disappointed and expressed sympathy to the victim's family.
"I am confident we presented sufficient evidence at trial to show Jason Stockley was guilty of murder in the first degree," she said.
The controversial ruling is the first major loss for Gardner's tenure as circuit attorney.
She was not in office when Stockley was charged or when Anthony Lamar Smith was shot and killed in 2011.
But Gardner inherited the high-profile case when she was elected to the office a first time last year.
She declined to say what she might have done differently had she been involved in the case sooner, but instead called for a new approach to officer-involved shootings.
Photos: Protests in St. Louis after Stockley decision
"The ability to have a comprehensive and independent investigation is critical to the unbiased pursuit of justice," Gardner said.
Currently, Gardner said St. Louis Police investigates their own officer-involved shootings. She said that practice needs to end.
"We need an independent and fair investigation in these cases because they're difficult. There's an uphill battle for officer-involved shootings," Gardner said.
She added the state should take another look at self-defense laws for law enforcement officers. "It's tough," Gardner said, referring to a prosecutor's duty to meet the burden of proof.
Doing nothing, Gardner said, would only reinforce what she called mistrust in the criminal justice system.
"I understand and know the deep mistrust for law enforcement and the criminal justice system as a whole in our communities and communities of color," she said.
Specifically, Gardner would like to see a third-party, independent group come in to investigate all of the city's officer-involved shootings.
She said that agency would be led by her office.