The newspaper also quoted three women as saying that one officer, Thomas Tolstoy, had sexually assaulted them. The assault allegations were examined in a separate probe and are still under investigation by the District Attorney's Office.
After years of investigation, federal and local authorities declined to press criminal charges against the officers. Federal authorities have declined to comment on the inquiry or its findings.
But investigative documents and interviews with people familiar with the case give a glimpse into how the four-year investigation was conducted, and why no one was charged with a crime.
The documents, which were summarized for The Inquirer, detail an inquiry that found patterns of suspected misconduct but fell short of exposing any crimes.
The investigation focused on allegations that officers in the squad lied about how they conducted drug operations. FBI and Internal Affairs investigators spoke to 10 informants - most of whom had never met each other - who described a pattern of apparent deception on warrants.
Trawling through hundreds of search warrants and arrest reports, investigators identified 11 warrants that seemed to contain false information, according to sources and documents.
But only one informant's story could be corroborated by multiple witnesses, the sources said - and none of the informants was willing to testify against the officers, they said.
In the documents, investigators detailed attempts to interview bodega owners who had told the newspaper that the officers had robbed them. But the owners either would not cooperate, did not have financial records of the missing cash, or could not provide proof of purchase for the allegedly stolen merchandise, the investigators said.
The store owners and their advocates have denied any reluctance to cooperate and said they believe there was sufficient evidence to build a criminal case.
In April 2009, at the height of the scandal touched off by the newspaper stories, investigators thought they had a potentially crucial break when, according to the documents, Tolstoy told the FBI he was willing to cooperate with the agency as an informant.
According to the documents, he said the allegations of misconduct reported in the articles were accurate. It is unclear what specific allegations he was referring to, although by that date, he had not been publicly accused of sexual assault.
One day later, according to the documents, Tolstoy's lawyer told the FBI that the officer would not work with them.
The lawyer, Mark Feinman, said Tuesday that Tolstoy had never raised the possibility of becoming an informant.
"He never discussed it with the FBI, and I never discussed it with the FBI," Feinman said.
He said FBI agents had visited Tolstoy's home, unannounced, and asked to speak with him about the newspaper stories. Tolstoy told the agents he would not speak to them without a lawyer, Feinman said.
Any reference to cooperation, the lawyer said, merely meant Tolstoy was willing to cooperate with any subpoenas or court orders.
"If they took that as he was going to be an informant, then shame on them," Feinman said.
On Monday, Philadelphia Police Commissioner Charles H. Ramsey announced that in the absence of any criminal charges stemming from alleged thefts or falsified warrants, the officers involved were facing departmental sanctions.
He fired Officer Jeffrey Cujdik for falsifying a warrant and having a business relationship with an informant. He suspended and transferred three other officers, and suspended a supervisor.
John McNesby, president of the Lodge 5 of the Fraternal Order of Police, said Tuesday that the union would contest the punishment. He said witnesses in the case were not credible and added that he "fully expects" Cujdik to get his job back through arbitration.
"These guys did nothing wrong," McNesby said. "They were doing their jobs."
The investigation into Cujdik's squad began in December 2008, when a longtime informant filed an Internal Affairs complaint about him. By January 2009, the FBI had taken the lead in the probe.
The first Daily News story on the squad appeared the next month, followed by a series of articles that won the 2010 Pulitzer Prize for investigative reporting.
According to the documents, the 10 informants interviewed by investigators all told roughly the same story: Their recollections of drug investigations did not match what the officers recorded on warrants.
Drugs the officers said were bought from one dealer had actually been purchased from another, the informants said.
On warrants, the officers credited the informants with giving information that had actually been supplied by others. Some informants said the officers had them sign blank vouchers and filled in the details later.
In interviews with Internal Affairs investigators, all of the officers denied wrongdoing and said they could not recall the events described by the informants, according to the documents.
The 11 warrants identified by investigators as questionable were filed by either Cujdik, Tolstoy, or Officer Robert McDonnell, according to the documents.
But in all but one of those cases, sources and documents said, discrepancies on the warrants were reported by a single informant and could not be corroborated.
In declining to prosecute, sources said the U.S. Attorney's Office said the informants had "problematic issues."
Some had given false statements to investigators, had ongoing drug problems, or were dealing drugs, the documents said. Some had mental-health issues. Some had criminal histories or were in trouble with the law. Some still held loyalties to Cujdik and the officers, while others seemed fearful of police.
A relative of the informant who had initially complained to police told investigators she suspected that the informant was lying about the officers out of anger because he had been evicted from a house Cujdik had rented to him, sources and documents said.
And, in perhaps the strongest blow to the investigation of the warrants, according to the documents, none of the informants was willing to testify in court. Other potential witnesses refused to be interviewed out of fear that their names would be reported in the media.
Investigators were similarly thwarted as they tried to verify accounts of bodega owners who said they had been robbed by Cujdik's squad during raids of their stores at which the officers searched for drug paraphernalia.
According to the documents, investigators' efforts to find bodega owners who would cooperate - or who had proof of the stolen items - proved difficult.
Investigators contacted Danilo Burgos, then the president of the Dominican Grocers' Association, and asked for his help in corroborating the owners' accounts, according to the documents. They said he never called back, according to the documents.
Burgos said Tuesday that he had given investigators contact information for about 20 bodega owners, and that he expected investigators to reach out to them and "do their job." He did not call back, he said, because he believed the evidence against the officers was "clear as day."
"We were just trying to help identify as many victims as possible," he said. "We turned over as much information as we received."
As for investigators' contentions that the bodega owners could not produce proof of the thefts, Burgos said, "They're trying to say it's the victims' fault."
He said that to his knowledge, two bodega owners had been interviewed by investigators. Those owners, he said, spoke briefly with agents, who promised to return with interpreters but did not.
Burgos said he found it "mind-boggling" that some of the officers had remained on the force. But he said he believed that Ramsey had "tried to do everything possible to bring these five bad cops to justice."
"Unfortunately, it's not much," he said of their punishment. "This is the citizens of Philadelphia losing out because of five bad officers."
Investigators interviewed one bodega owner at length, according to the documents. He had captured video of officers dismantling security cameras at his West Oak Lane grocery while carrying out a warrant. He said that after the wires were cut, the officers stole about $10,000 that he had been keeping in a cigar box and a book bag to pay bills.
According to the documents, the bodega owner did not cooperate when investigators attempted to corroborate his account of the theft.
Internal Affairs investigators later concluded that dismantling the security cameras had not violated department policy because at the time there was no policy on cutting camera wires. The officers said it was standard procedure to cut the wires of surveillance cameras to protect the identity of plainclothes officers.
Attempts to persuade the accused officers to cooperate with investigators and give statements were unsuccessful, according to the documents.
One promising lead came when FBI agents met with Tolstoy at his home, the documents said.
In an April 2009 meeting with agents, Tolstoy said the allegations in the Daily News stories were accurate, and agreed to cooperate with the FBI as an informant as early as the next day, according to the documents.
The documents do not specify which of the articles' allegations Tolstoy was referring to. By that date, the newspaper had published stories on the alleged bodega thefts and falsified warrants. It also had published a woman's account of a sexual assault during a drug raid, but did not name Tolstoy.
In later stories, that woman and two others identified Tolstoy as the officer who had groped their breasts during raids. One of the three said he had put his finger in her vagina as he searched her for drugs.
Tolstoy has denied any wrongdoing.
The documents do not make clear to what extent Tolstoy had been prepared to cooperate, or if he had agreed to give statements incriminating anyone.
Investigators never got a chance to find out.