Ethnic Indians in Malaysia on Wednesday marked the annual Hindu festival of Thaipusam, declared as a national holiday in Malaysia for the first time, but a boycott call linked to alleged discrimination against the community and fears of violence kept many away from the celebrations.

Worshippers, some with hooks and spears pierced through their bodies, thronged Hindu temples across the country while more than 40,000 climbed the famous Batu Caves, which houses the Sri Subramaniar temple of Lord Murugan (Kartik), in the outskirts of Kuala Lumpur.

Every year, at least a million Hindus visit Batu Caves on this day, but this year the crowd seemed to be much lesser in number. Other than the boycott call by Indian activists, rumours that violence could break out also kept people away.

Some worshippers said devotees were asked to attend prayers at other temples instead of Batu Caves, which is controlled by the Malaysian Indian Congress, a partner of the ruling Barisan Party.

Indian activists accuse the MIC of not doing enough for the community. Text messages criticising the party did rounds before the festival.

MIC president Samy Vellu, however, did not see any drop in the crowds visiting Batu Caves, saying that at least one million had come. "The crowd is the usual crowd. I have come to Thaipusam for 60 years... I am very very happy," he said.

"I don't think religious people who went to pray to Lord Murugan will listen to all the naughty fellows," Vellu said of the SMS campaign.

"Who can threaten us? Anyone who threatens us we can find out where he is. It takes only five hours to find out where he is. They can't run away from us."

Some 20,000 ethnic Indians rallied in Kuala Lumpur on November 25 on a call by non-governmental organisation Hindu Rights Action Front to raise their grievances over alleged discrimination in the Muslim-majority country.

The government has denied the allegations.

Five leaders of Hindraf remain behind bars on charges of threatening public security and inciting racial hatred. In a move to assuage the feelings of agitated ethnic Indians ahead of elections, the Malaysian prime minister has declared the Thaipusam festival as a national holiday.

Thaipusam is a major Hindu festival among Indians in Malaysia and Singapore where devotees offer prayers to Lord Murugan.

Hundreds of youth carried 'kavadi' (decorated wooden frames) over their shoulders while going up the 172 steep steps of the Batu Caves. Men, women and children attired in new clothes balanced pails of milk on top of their heads heading towards temples.

Ethnic Indians form 7.8 per cent of Malaysia's 27 million people of which 60 per cent are Muslim Malays while 25 per cent are ethnic Chinese who are Buddhists or Christians.