Two of the bags were found on the tarmac, but the third remains missing.
A Hong Kong Police spokesman said the airport police crime unit was leading the investigation. No information could be released.
Cathay Pacific spokeswoman Tracey Kwong confirmed that the airline had transported the "valuable shipment".
G4S International Logistics - which specialises in transporting valuable cargo internationally - denied responsibility for the lost money, which is insured. The company's North Asia commodities director, Janet Leung, said the entire currency consignment was accounted for before its transfer into a restricted area at the airport.
"This loss occurred within the controlled airside sector of HKIA - a restricted area that we are not allowed access to," she said.
"We can confirm that the missing banknotes were safe and accounted for during the entire time it was in G4Si's possession, up until it was in the controlled airside sector."
Police and Customs officials in New Zealand were aware of the investigation but were not involved.
A Customs spokeswoman said the cash consignment was freight so needed to have special clearance to leave New Zealand. She said there was no issue with the money leaving New Zealand.
Privacy laws prevented Customs from detailing who sent the cash to Hong Kong.
Bank warns on sending large sums
The case of the missing money has prompted a local bank to warn New Zealanders against sending large sums of cash overseas.
A BNZ spokeswoman said it was advisable for people to use internet banking or financial institutions when transferring cash abroad.
"Our recommendation is if people need to move large sums of money in between countries, that they transfer it through a robust financial system.
"Also it's easier because it means people don't carry large amounts of cash and it means the money can be traced."
BNZ said individuals who chose to travel with paper money were responsible for checking relevant customs regulations and local laws.
In New Zealand, prohibited items cannot be sent in the post unless NZ Post agreed in writing to carry them.
These prohibited items included traveller's cheques, deeds, "negotiable instruments", bonds or shares, credit or bank cards, coins and currency or precious metal.
In Britain, Royal Mail said it would not accept liability for loss or damage to mail items containing money sent to 50 countries, including New Zealand and China.
- NZ Herald, NZME.