The Environmental Crime Prevention and Fighting Police Department tracked down the contraband in collaboration with the city police.
The warehouse belongs to the state-owned Sai Gon Cargo Service Corporation.
The horns had been sent to Vietnam from the Philippines in 12 packages for onward shipment to other countries with a bill of lading each from Singapore Airlines and Cathay Pacific Airlines.
The police did not disclose the identities of the consignors or consignees, but have said they will probe into the horns’ origin, now assumed to be Africa.
If they are indeed African rhino horns, they are worth more than VND40 billion ($1.72 million) on the black market, according to the police.
The international trade in rhino horn has been banned since 1977 under the Convention on International Trade of Endangered Species.
Yet, according to U.K. conservation charity Save the Rhino, individual countries are able to determine whether to allow or prohibit the sale of rhino horn domestically.
It is banned in Vietnam, but the country remains one of its biggest consumers with people believing it has powers to cure diseases like cancer. Rhino horn consumption is also a sign of status.
Last month a HCMC court sentenced a man to six years in jail for illegally transporting over six kilograms of rhino horns from Mozambique.