The shipment was sent by a Nigeria-based company called Mercury Resources Ltd to Pama Northern Trading Import Export Company Limited in Hanoi, customs said.
The sender had registered the content of the containers as 56 wood logs. But it had 330 kilograms of elephant tusks and 1,700 kg of pangolin scales.
The shipment arrived but the recipient did not come to the VIP Green Port in the northern city Hai Phong for many days to claim it.
On December 10 customs officials and the city police opened the containers and discovered the illegal items.
Authorities have not been able to track down Pama Northern leaders or its legal representative and said the company does not operate at the address stated in its business registration.
They are investigating.
Vietnam outlawed ivory trade in 1992, but the country remains a top market for ivory, which is prized for decorative and medicinal purposes, according to conservation groups.
Likewise, pangolins are legally protected and categorized as endangered in the country, but trafficking of the animal is not rare.
The shy, tiny creature, which resembles a scaly anteater, is hunted in Vietnam and its neighborhood for its meat and the alleged medicinal properties of its scales.
Pangolins are the world's most heavily trafficked mammal despite bans.
Vietnam is among the top 10 countries and territories in terms of trafficking incidents, according to a December 2017 study by wildlife trade monitoring group TRAFFIC and Australia’s University of Adelaide.
Mainland China, Malaysia, Hong Kong, Thailand, Laos, and Indonesia also make the list.