The 23-year-old son was among the eight people questioned after the raids.
Shah Rukh Khan was seen leaving his home and heading for his lawyer's office shortly before the arrest was confirmed, reports NDTV.
The high-profile raid yielded 13 grams of cocaine, 21 grams of charas and 22 pills of MDMA, the NCB has said. The charges brought against Aryan Khan include purchase, possession and use of banned substances, NCB said.
"All eight, including Aryan Khan, are being questioned. Based on their statements further action will be taken," the anti-drugs agency had said earlier in a statement.
There were two women among the eight questioned. The eight people were Munmun Dhamecha, Nupur Sarika, Ismeet Singh, Mohak Jaswal, Vikrant Chhoker, Gomit Chopra, Aryan Khan, Arbaaz Merchant.
Of the eight, three, including Aryan, were taken for a medical test.
The NCB team boarded the Goa-bound ship on Saturday night disguised as passengers, sources said. According to officials, the party began after the ship left Mumbai and was at sea.
During the operation, the suspects were searched and different drugs were recovered from them, which they had hidden in their clothes, undergarments and purses, an NCB official told news agency PTI.
"Their statements are being recorded. Based on the facts, arrests will be made and the accused will be produced in the NDPS court," a senior NCB officer told NDTV.
The cruise company in a statement on Sunday said it had nothing to do with the incident.
The NCB said it had raided the cruise as it had information that a rave party was going to be held at the cruise and some people associated with the film industry might be present. The NCB had information that drugs will be used at the party, Hindustan Times reports.