The NCB had on October 3 arrested actor Shah Rukh Khan's son Aryan, Merchant and some others after raiding a cruise ship here and allegedly recovering drugs.
The court said that perusal of the WhatsApp chats extracted from the phone of Aryan Khan shows that nothing objectionable was noticed to suggest that accused hatched a conspiracy.
Merchant and Kumar arrived at the NCB office in south Mumbai separately around 11:30 AM-12 noon. They were allowed to go after 9 PM.
Sources said the agency has found "certain issues" in the probe in these six cases and hence they are being taken away from the Mumbai unit.
The court in its detailed order, a copy of which was made available on Sunday, also raised questions on the veracity of the Narcotics Control Bureau's (NCB) panchnama records.
Earlier in the drug-on-cruise case, Maharashtra Minister Nawab Malik had accused Sameer Wankhede of favouritism.
While Aryan Khan was released from the Arthur Road jail on October 30, Dhamecha walked out of the Byculla women's jail here around 11 am on October 31.
Cruise drugs case: PIL in SC seeks CBI probe, direction to Centre to frame witness protection scheme
The case involves Bollywood superstar Shah Rukh Khan's son Aryan Khan and others as accused and has triggered a series of controversies and put the bureau and its officials under the spotlight.
Drugs case: Aryan Khan set to walk out of Arthur Road prison after officials collect his release papers
While granting Aryan bail on Thursday in the drugs-on-cruise case, the Bombay High Court imposed 14 bail conditions on him, paving the way for his release from jail.
Taking to her Instagram Story, Pooja wrote, "There is a God...thank you everyone for your love and prayers. Truth prevails."
A single bench of Justice N W Sambre also granted bail to Aryan Khan's co-accused Arbaaz Merchant and Munmun Dhamecha.
The two co-accused -- Arbaaz Merchant and Munmun Dhamecha -- will also be released on Friday as they got bail along with the star kid.
However, the special Narcotics Drugs and Psychotropic Substances (NDPS) court is hearing a plea for bail to Aryan Khan, Arbaaz Merchant and Munmun Dhamecha in the matter.
The NCB sought the custody of Aryan Khan Arbaaz Merchant till Monday citing recovery of 2.6 grams ganja from them and name of the supplier.