Officers allegedly found about 5kg of a white powdery substance, which tested positive for cocaine, concealed in a suitcase inside a cabin occupied by Wilkinson and Harris, both New Zealand citizens.
A further 7.7kg of cocaine was allegedly found in a cabin belonging to 27-year-old Australian Ahmed Rachid, the US Department of Homeland Security said in a statement.
Customs Border Patrol spokesman Gary Horne said that during an interview with Rachid, officers detected an "anomaly'' which prompted a search of his cabin, UK's The Mirror reported.
"We talk to them. We ask them where they're from and what they're bringing in,'' he said.
All three were arrested by Immigration and Customs Enforcement officials for investigation of possession with intent to distribute cocaine.
Customs inspectors would no say if the two discoveries were related, said The Mirror.
The Ministry of Foreign Affairs said today it had offered consular assistance to the New Zealanders.
The spokesman would not say if they were in custody.
The three people are understood to have been aboard the Aurora during a world cruise and had arrived in San Francisco from Curacao, a Caribbean Island.
After leaving San Francisco it sailed to Honolulu, and was now on its way to Sydney.
A P&O Cruises spokesman said he could not comment on an ongoing investigation.
