Batista, 34, pleaded "absolutely not guilty" on Thursday to drug dealing, obstructing justice and other charges, and was expected to be released on $500,000 bond before the weekend. Conde, 34, had pleaded not guilty following his arrest last year.
"If in fact these accusations prove to be true, it's despicable conduct," Police Commissioner Raymond Kelly said following a promotion ceremony at police headquarters.
The federal indictment follows the recent arrests of another detective in the prostitution case and of four more officers in Brooklyn on charges they secretly used money and drugs seized during arrests to pay informants.
Police officials have claimed the corruption cases, while troubling, were unrelated aberrations at the 35,000-officer NYPD.
"Unfortunately the sad reality is that you're always going to have, in that universe of people, some individuals who will violate the public trust," Kelly said.
In the latest case, internal affairs and federal investigators say they unearthed evidence that Batista was part of a drug-dealing operation run by old friends. His attorney, James Moschella, admitted his client knew the dealers and sometimes used them as informants, but said he never committed crimes with them.
On Wednesday, Detective Wayne Taylor and a woman accused of working as his partner pleaded not guilty in Queens to kidnapping, promoting prostitution, assault and endangering the welfare of a child. Prosecutors allege the pair took their 13-year-old victim to parties throughout the city, where about 20 men paid to have sex with her before she escaped to her family.
A third ongoing corruption case in Brooklyn so far has resulted in four officers being arrested, others suspended and their superiors stripped of their commands. The investigation was launched last year after an undercover detective mistakenly revealed on a recording that he and another officer had forged paperwork about a drug arrest, saying that 17 bags of cocaine were seized instead of the real total, 28.
Internal affairs investigators say they later learned that after a seizure of 40 bags of cocaine and $250 in November, two other officers stole two bags and $40 to give to an informant as a reward.