The structure is to be built in the Betong district of the southern province of Yala, one of the three southern provinces bordering Malaysia.
The former prime minister, Thaksin Shinawatra, infuriated Kuala Lumpur in 2005 when he suggested building a security wall along the entire 500-km border with Malaysia to stop separatist supporters from crossing the border.
Malaysia has repeatedly denied assertions by Thai security agencies that separatist fighters are hiding on its territory.
Surayud said there was no need to run the proposal by the Malaysian prime minister, Abdullah Ahmad Badawi, who will visit Thailand for annual bilateral talks on February 11.
"If we don't build it, it could disadvantage us because we will face problems with border crossings and smuggling," he said after meeting with Betong's mayor, whose district is considered a centre of separatist activity.
Nobody has claimed responsibility for the violence which has seen almost daily gun and bomb attacks in the three predominantly Muslim southern provinces where many people hold dual Thai-Malaysian citizenship.
Surayud's weekend visit is part of a peace drive in the Malay-speaking region, an independent sultanate until the Buddhist-dominated Bangkok government annexed it a century ago.
But the attacks have continued, including one on an ice-cream vendor who was shot dead and beheaded on Thursday in the neighbouring province of Pattani.