"Our department is shaken," an emotional San Francisco Police Chief Greg Suhr said on Thursday.
Suhr said the scandal would make it hard for his officers.
"I will not have dishonest cops among us," he said. "As they sully the ranks of honest men and women out there doing their jobs."
George Gascon was district attorney when federal authorities launched their probe.
"When members of the law enforcement community violate the law, they themselves become criminals," he said. "We cannot tolerance for that behavior."
Three of those indicted are officers at Southern Station. Two others are assigned to the Mission. The sixth defendant, Reynaldo Vargas, was dismissed from the department for an unrelated offense.
The indictments ended a three year investigation by federal authorities. It was a probe that was launched when Public Defender Jeff Adachi released security camera video from residential hotels. Adachi charged that the videos showed the officers violating suspects' rights under the color of law. The officers from Southern Station were on two separate videos from the Henry Hotel.
"These officers were barging into their rooms without warrants and lying about it in police reports," Adachi said.
Vargas, from Mission Station, was captured on video from the Jefferson Hotel. The indictment charges him and the other two Mission Station officers with distributing marijuana, stealing money and personal property.
"The indictment today is a victory for ordinary San Franciscans," Adachi said.
Police Officers Association President Martin Halloran said not so fast.
These are only indictments," he said. "These officers are now going to be afforded their rights to tell their side of the story."
In an exclusive interview with ABC7 News, Halloran and lawyer Michael Rains warned against jumping to conclusions.
"If it was in fact informants, street informants, I would question their consistency and reliability," Halloran said.
"My feeling right now is they finally made a case after three years; that tells me something about the evidence they have, I don't think it's probably great, I don't think it's much," Rains said.
The officers have been disarmed and suspended without pay. Vargas pleaded not guilty in court Thursday; the officers will appear in court Friday.