The contraband was found in two separate raids in the cargo terminal of Kuala Lumpur's main international airport on Sunday, customs officials said.
In the first raid, authorities found 23 ivory tusks, weighing 75.7 kilograms (167 pounds) with an estimated value of 275,000 ringgit ($64,150).
"Customs officers seized two boxes which contained a large quantity of elephant tusks," senior customs official Pudzi Man said in a statement.
The tusks had been sent from Nigeria, and the cargo was listed as food items, he said.
Separately, officials found six sacks containing 300.9 kilograms (663 pounds) of pangolin scales worth 3.86 million ringgit ($900,500), said Pudzi. The cargo had originated in the Democratic Republic of Congo.
No arrests have yet been made over the seizures.
Elephant tusks are in high demand in parts of Asia, especially China and Vietnam, where the ivory is prized for decorative purposes and in traditional medicine. The global trade in elephant ivory, with rare exceptions, has been outlawed since 1989.
The scales of the pangolin, a critically endangered creature also known as the "scaly anteater" that is the world's most heavily trafficked mammal, are highly sought after in some Asian countries for use in traditional medicine.
Pangolin meat is considered a delicacy in China and their scales are also sometimes used in the production of crystal methamphetamine.
The seizures underline Malaysia's role as a major transit point in the global wildlife smuggling trade. Last month, a Vietnamese man was arrested at Kuala Lumpur airport and a large stash of elephant ivory found in his luggage was seized.
Anyone found guilty of importing rare animals or their parts into Malaysia can be jailed for up to three years and fined.
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