The anti-drugs agency has filed a 6,000-page charge sheet, naming 14 accused, after drugs were found in a raid on a cruise ship off Mumbai last year.
Aryan Khan, 23, who was one of several people arrested following the raids in October, has not been named as an accused.
"All the accused persons were found in possession of narcotics except Aryan and Mohak," read a statement by senior NCB officer Sanjay Kumar Singh.
The agency could not find sufficient evidence against Aryan Khan and the five others, he said.
Aryan Khan had spent more than three weeks in jail after he was arrested in the drugs case that dominated news headlines and polarised social media.
The Narcotic Control Bureau had claimed Aryan Khan was a regular user and supplier of drugs.
The charges were strongly denied by him and his lawyers who contended that no drugs were found on him during the raid.
The officer in charge of the investigation, Sameer Wankhede, was dropped amid allegations of deliberately targeting Aryan Khan and even trying to blackmail the accused.
The case was also transferred from a Mumbai-based team of the NCB to a Delhi-based team after irregularities and lapses in the probe emerged.