Philadelphia Police Commissioner Charles Ramsey had asked the FBI to investigate the allegations in the 2009 "Tainted Justice" series by the Philadelphia Daily News.
Ramsey said Thursday both the U.S. attorney and district attorney declined to prosecute.
The newspaper detailed cases in which officers allegedly stole from corner stores during raids, lied and mistreated suspects. Its series won the 2010 Pulitzer for investigative reporting.
The officers could still face discipline. An Internal Affairs investigation has sustained several allegations, the commissioner said.
The police union said the newspaper wrongly cast the officers as rogue cops.
"It was death by headlines," John McNesby, local Fraternal Order of Police president, told the Daily News. He said the union would also defend the officers against the internal charges.
Daily News editor Michael Days said the newspaper stands by its stories by reporters Wendy Ruderman and Barbara Laker, who have also written a book about their work, "Busted: A Tale of Corruption and Betrayal in the City of Brotherly Love."
"We're disappointed, obviously," he told the Daily News' sister paper, The Philadelphia Inquirer, "but the citizens of Philadelphia should be even more disappointed."
The U.S. attorney's office would not comment on its decision.
In a prepared statement, the district attorney's office said that it decided to accept the judgment of federal prosecutors given they had "exhaustively investigated" the case over a period of years.
Ramsey told the Inquirer that the department would not have brought the allegations to prosecutors "if we didn't think it was a good case."
Dozens of lawsuits were filed against the city in the wake of the series. The city settled 33 and paid out $1.7 million.