Buddhist groups held special prayers on Sunday at a Kuala Lumpur temple to call for a trouble-free run.
About 300 Chinese students studying in Malaysia greeted the flame at the airport along with representatives from the National Sports Council and the police, a statement from the Olympic Council of Malaysia said.Olympic 'challenges'
The torch will be taken along a 16km route from Independence Square to the Petronas Twin Towers in downtown Kuala Lumpur. Roads will be closed to traffic along the route.
M. Jegathesan, vice president of the Olympic Council of Malaysia, said that police were "fully aware of the challenges that this torch has faced in other situations, and they have been organising themselves to face any of these challenges".
On Friday, about 30 Falun Gong practitioners demonstrated in Kuala Lumpur, calling for an end to alleged Chinese human rights abuses before of the Beijing Olympics.
The international torch relay has been marred by protests over China's crackdown in Tibet.
The Thailand leg of the torch relay employed more than 2,000 police and security officials to guard the flame, with thousands of people coming to watch the event.
A group of about 60 people protested by waving pro-Tibet banners outside the UN headquarters in Bangkok about 3km from the relay route.
A similar sized crowd of pro-Chinese protesters were also at the same site waving the Olympic flag and shouting pro-Chinese chants.
Police kept the two groups apart.
Meanwhile, a Buddhist temple in Japan has been vandalised just days after officials halted plans to host the upcoming Olympic torch relay.
Authorities from the Zenkoji temple decided to pull out of the event citing sympathies with Tibetan protestors facing a crackdown by Chinese authorities.
White circular patterns and lines were sprayed in several places over the Zenkoji Temple. Police are investigating the incident.