Preet Bharara, the U.S.attorney for the Southern District of New York, said he personally informed the family of Ramarley Graham and their representatives of the decision to not prosecute New York Police Officer Richard Haste.
Graham's family denounced the decision.
"Same as usual -- black lives don't matter," said Graham's father, Franclot, according to CNN affiliate NY1 News
. "Ramarley's life will always matter to us."
The shooting occurred in the Bronx on February 2, 2012, after Graham ran to his home with officers in pursuit, prosecutors said.
Haste told investigators that when he confronted Graham in the bathroom, the teen had his hand in his waistband, Bharara said in a statement.
The young man made a motion and Haste told investigators "he believed that Mr. Graham was reaching for the weapon that had been described in [an] earlier radio transmission, and that he fired one round from his weapon in response to a perceived deadly threat," according to the statement.
No gun was found at the scene, prosecutors said. A bag of marijuana was in the toilet bowl next to where Graham had stood.
Federal prosecutors "determined that there is insufficient evidence to meet the high burden of proof required for a federal criminal civil rights prosecution," Bharara said in the statement.
"To prove a violation of the federal criminal civil rights statute, prosecutors must establish, beyond a reasonable doubt, that a law enforcement officer willfully deprived an individual of a constitutional right, meaning that the officer acted with the deliberate and specific intent to do something the law forbids," Bharara said.
The officer's actions had to be considered "in light of his knowledge at the time of the shooting," and no evidence refuted Haste's claim he shot Graham in the mistaken belief the teen was reaching for a gun, Baharra said.
Graham's family, their lawyer and local officials voiced disappointment with the decision.
"The family is devastated and frustrated," said Jeffrey Emdin, a lawyer representing the Graham family.
The family has demanded that Haste be fired immediately. The officer has been on desk duty while NYPD Internal Affairs investigates the shooting.
Last year, family received a $3.9 million settlement in a wrongful death lawsuit against the city, Emdin said.
Bronx Borough President Ruben Diaz Jr. said he was "deeply saddened and extremely shocked" by the decision.
"My heart goes out to the Graham families, who have now seen their quest for justice for their son twice denied," Diaz said in a statement.
In 2013, a Bronx Supreme Court judge dismissed a manslaughter indictment against Haste
based on instructions given by the prosecution to the grand jury regarding communications among officers before the shooting.
"This latest development is an outrage," Diaz said. "At a time when the issue of police-community relations has been at the forefront of American discourse -- especially the treatment of minorities by those charged to protect and serve them -- the U.S. attorney's office has failed to set an example for our nation."
Stuart London, Haste's attorney, said his client looks forward to resolving the police department's internal investigation.
"My client is gratified that he will not face a federal civil rights prosecution," London said. "There are no winners when there is a loss of life.
In the criminal case that was eventually thrown out, the indictment alleged that Haste acted "recklessly" and killed Graham "with intent to cause serious physical injury."
But in dismissing the case, Judge Steven Barrett said the grand jury was told "by both commission and omission" that communications of other officers with Haste "were not relevant."
After Barrett read his decision, Constance Malcolm, Graham's mother, yelled, "He killed my child!"
Graham's family said he was shot as his grandmother and his 6-year-old brother looked on.