"Although religious in nature, the Thaipusam celebration in Malaysia showcases to the world our diversity with Malaysians respecting and accepting each other's culture, religion and beliefs," Najib wrote on his official website.
"We must continue to uphold these noble principles to further strengthen our solidarity and national unity in the true spirit of Malaysia."
The country of roughly 29 million people has a majority population of Malays who are all Muslims, 25 per cent ethnic Chinese, mostly Christians or Buddhists, and eight per cent ethnic Indians who are mostly Hindus.
Kavadi, meaning "sacrifice at every step", can weigh as much as 100 kilogramme and are typically affixed to a person's body using sharp metal spikes.
Many devotees sported long metallic skewers stuck through their flesh in a form of penance, attracting huge attention.
Thaipusam is a combination of the name of the Tamil month "Thai" and the star "Pusam" which is said to be at its highest point during this festival.
Thaipusam is celebrated with great pomp in the northwestern Penang state. This year, the grand Silver Chariot used in the Thaipusam celebration there is reportedly 120 years old.
The Lord Murugan idol inside the chariot, weighing 4 kgs, is 160 years old and ismade of five precious metals - gold, copper, silver, tin and brass - and is studded with diamonds and gems.
"Lord Muruga is depicted standing on a golden peacock, his favourite animal, and beside him is a small gold statue of Lord Ganesha, his brother," a temple trustee in Penang said.