Previous legs of the torch relay in Europe and the US, as well as the flame lighting ceremony in Greece, were targeted by protests against China's recent crackdown on unrest in Tibet.
Police said they have not received reports of any planned protests from pro-Tibet groups but will nonetheless deploy around 1,600 policemen to secure the 16.5-kilometre route and close roads along route.
The Olympic flame arrived in Kuala Lumpur early on Sunday on a flight from Thailand before being whisked off to a hotel for safekeeping.
It was received by China's ambassador to Malaysia, officials from the Olympic Council of Malaysia and representatives from the country's sporting bodies.
Some 300 Chinese students studying in Malaysia were also at the airport with representatives from the National Sports Council and the police.
Prayers and protests
On Friday about 30 practitioners of Falun Gong, a spiritual movement outlawed in China, protested in Kuala Lumpur calling for an end to alleged Chinese human rights abuses.
The group, which Beijing has labelled a dangerous cult, is not banned in Malaysia.
Buddhist groups in Malaysia also held candlelight vigils at temples over the weekend to pray for a trouble-free torch run and a peaceful Olympics.
Rais Yatim, Malaysia's foreign minister, said the hosting of the torch relay reflected the nation's close bilateral ties with China and for the Olympics to be kept separate from political issues.
"Malaysia takes this opportunity to reiterate that the Beijing Olympics should not be politicised and remains confident that the Olympics will be successfully held in August 2008," he said in a statement.
The symbol of the 2008 Beijing Olympics is on the Asian leg of its world tour after anti-China protests disrupted parts of the relay in Europe and the United States earlier this month.
Those protests triggered a backlash in China in recent days, with reports of anti-Western demonstrations in several Chinese cities.
Several branches of the French supermarket chain Carrefour were blockaded by protesters angry at disruption to the Paris leg of the torch relay and suggestions by the French president that he may boycott the Olympics opening ceremony in August.
In a separate development, Japanese officials have reportedly chosen a new route for the Olympic torch relay after a major temple pulled out of the plans over security concerns and sympathy for Tibetan protesters.
Kyodo News and national broadcaster NHK said Nagano city officials will start the April 26 leg of the relay at a city-owned parking lot instead of the temple.
Buddhist monks at the centuries-old Zenkoji temple refused to host the start of the relay.
Vandals over the weekend spray painted the temple with white paint, though officials would not say whether the two events were related.
After Malaysia, the Olympic torch relay will be making stops in Indonesia, Australia, South Korea, Japan and Vietnam before heading to China.