A judge has dismissed manslaughter charges against a New York City police officer who shot dead an unarmed teenage boy in his bathroom.

Bronx supreme court justice Steven L Barrett said the Bronx district attorney's office failed to properly instruct members of a grand jury in considering allegations against officer Richard Haste for his role in the death in 2012 of 18-year-old Ramarley Graham.

"With no great pleasure, I am obliged in this case to dismiss the charges," Barrett said in an emotional hearing Wednesday morning, according to the news website DNAInfo. He made it clear that the dismissal was because of a failure to follow procedure, not because of the evidence. "This is not a case where there is insufficient evidence," the judge said.

The charges against Haste were the first of a NYPD officer relating to a fatal shooting on duty since 2007. Then, three detectives were charged over the death of a man shot after he left a strip club on the eve of his wedding. The three were later found not guilty.

Graham's mother, Constance Malcolm, cried out before leaving the courtroom in tears on Wednesday: "He killed my child. What more can you do to me?"

Haste shot and killed Graham in his apartment bathroom on 2 February 2012 while his six year-old brother and 58 year-old grandmother looked on. His attorney, Stuart London, has maintained that because of radio calls that preceded the shooting, his client was under the impression that Graham was armed and only fired after repeatedly ordering the teen to show his hands.

In June, Haste turned himself in and was arraigned on charges of first- and second-degree manslaughter.

Last week, judge Barrett said he was "officially concerned" by the grand jury minutes that resulted in Haste's indictment. Barrett said the minutes indicated jurors were erroneously told to disregard whether Haste was under the impression Graham was armed.

The NYPD initially claimed Graham ran from officers after he was spotted near his home, but surveillance footage from the property later showed him calmly entering his apartment seconds before men in NYPD windbreakers ran up to the front door with their guns drawn. The officers forced their way inside and Haste made his way to the second floor where Graham was killed. No weapon was recovered, though a small bag of marijuana was found in the toilet bowl. Subsequent reports revealed Haste did not receive the requisite training needed to work with the aggressive anti-drug unit he was assigned to.

His attorney, Stuart London, has maintained that his client was under the impression from radio calls preceding the incident that Graham was armed and only fired after repeatedly ordering the teen to show his hands.

During Wednesday's half-hour hearing, judge Barrett said his ruling does not prevent the case from being presented to the grand jury again.

Speaking to the Guardian by phone Wednesday morning, Frank Graham, the teenager's father, was clearly shaken by the judge's ruling. "I don't know what to say," he said. "Right now we are angry. We are upset and very disappointed."

Ramarley Graham's mother, Constance Malcolm, was taken to a hospital following the judge's decision, Graham said, after she found herself struggling to breathe. "Everything just overwhelmed her," he said.

The family plans to press for another indictment. "It doesn't end there," Graham said. "They are going to convene a new grand jury and we are going to get Richard Haste indicted again, for a second time, and he [will] be convicted for killing our son."

Graham said he wants his son to be remembered as a "loving, caring, respectful" boy. "Ramarley had passion for helping people," he said, noting the teen's tendency to stay home with his younger siblings. "He loved staying with [the] younger ones and playing with them and just babysitting."

"Unfortunately he was murdered by someone who didn't respect the law," Graham said.

The Bronx district attorney will now decide whether to appeal the decision or represent the indictment. The district attorney's office said in a statement: "It cannot be said more forcefully that we disagree with the court."