The Southeast Asian nation is battling to clamp down on rife trafficking through its borders of the ant-eating mammals, whose scales are highly valued in traditional Chinese medicine.
"Such a huge seizure and torching of it is definitely a blow to smuggling syndicates," Abdul Kadir Abu Hashim, the director-general of the Wildlife and National Parks Department told AFP.
Some 3,000 pangolins would have been killed to obtain the 2.8 tonnes (2,800 kilograms) of scales, Abdul Kadir estimated.
The scales were confiscated by customs officials at Malaysia's Port Klang between May and September 2017.
The animal parts arrived in three different shipments from Ghana and Cameroon, and had false local addresses, officials said.
"Forensic examination of the scales showed that it is from the African species," said Abdul Kadir.
The scales were incinerated at a private waste disposal plant in Port Dickson, Negeri Sembilan, south of the capital Kuala Lumpur.
Seized pangolin scales are usually meant for foreign markets including China and Vietnam, where raw pangolin scales are sold for large profits in traditional Chinese medicine.
Last year Malaysia torched eight tonnes of pangolin scales, Abdul Kadir said, adding that wild pangolins in Malaysia have become a rare sight due to rampant hunting and deforestation.
Pangolins are also heavily poached for their meat which is considered a delicacy while products obtained from the animal are thought to increase blood circulation and lactation.