Without providing details, he also cited allegations that "they intentionally fabricated parts of their story."
H.F. "Gerry" Lenfest, owner of the company that publishes The Inquirer and the Daily News, rejected the criticism.
"We stand behind the work of our reporters and have seen no 'sound evidence' that their work was anything but thorough, accurate and ethical," he said in a statement.
He added: "Our company does not take allegations of unethical behavior lightly, and I can assure Mr. McNesby that if such 'sound evidence' exists, we will pursue it."
The 2009 stories by Daily News reporters Barbara Laker and Wendy Ruderman reported that members of the Philadelphia police narcotics division had lied on search warrants and stolen from bodega owners during raids. The articles said that one officer, Thomas Tolstoy, had sexually assaulted three women during drug raids.
In the spring, after years of investigation, federal prosecutors said they would not bring criminal charges against any of the officers in connection with alleged thefts or illegal searches.
One of the alleged sexual assaults remains under investigation by the District Attorney's Office; the statute of limitations has expired on the two others.
Ramsey said any financial assistance provided to the key witness - a woman who alleged that Tolstoy had put his finger into her vagina - would undermine the reporting of her account.
"My understanding is that for one of the people who was a witness against officers in the case, the reporters actually paid utility bills, bought gifts, dinner, and things of that nature," he said.
"It would seem to me that would possibly taint the investigation. It would certainly lead one to question if all the information being provided is accurate or is it being provided because of favors."
Ramsey also said he was disappointed at reports that The Inquirer had declined to publish an article that explored the allegations involving the Daily News reporters.
Ramsey and McNesby said The Inquirer or the Daily News should investigate the reporters' conduct. McNesby also suggested that the Pulitzer board should look into the matter.
Daily News editor Michael Days declined to comment Wednesday, deferring to Lenfest, as did reporters Laker and Ruderman.
During a news conference at FOP headquarters, McNesby said the five officers implicated by the stories had undergone an ordeal during the five years they were put on desk duty and investigated.
"After years of unsupported whispers and suspicion, all of the officers were cleared of any wrongdoing. They were absolved entirely," he said.
McNesby brushed aside the internal discipline Ramsey imposed on the officers, predicting that it would be reversed by arbitrators.
Four officers, including Tolstoy, were suspended for a month for a variety of offenses, including fabricating search warrants, carrying out an illegal search, and giving informant gifts, such as money, cigarettes, cellphones, and prepaid phone cards.
Ramsey fired a fifth officer, Jeffrey Cujdik, after Internal Affairs determined that he lied to investigators, falsified a search warrant, and rented a room to an informant, a violation of rules forbidding business dealings between police and informants.
Thomas W. Jennings, a lawyer for the FOP, said Wednesday that the union had already won an arbitration decision that Cujdik had been improperly removed from street duty during the long investigation. Jennings said that should clear the way for him to be paid about $200,000 for years of lost overtime.