More than 2,000 people have died since violence first flared up in Thailand's south in early 2004.
Peace and security
|Syed Hamid said terrorists must not be allowed |
to take advantage of the situation[EPA/file]
Although the troubles have not yet flared into a regional problem, Syed Hamid said it was important enough to address "in ensuring peace and security in the region".
"It may not have spilled over but Asean, or the Association of Southeast Asian Nations, must look at certain security matters as one whole region," he said.
"We hope that they will find a way that will not allow for any terrorist groups to take advantage of the instability or unhappiness."
Western intelligence analysts have previously suggested that operatives of Jemaah Islamiyah, a regional militant group with alleged links to al-Qaeda, could move into southern Thailand to take advantage of the prevailing unrest.
Jemaah Islamiyah is accused of carrying out a string of attacks in South-East Asia, including the 2002 Bali nightclub bombings.
On Monday Abdullah Ahmad Badawi, Malaysia's prime minister and his Thai counterpart, Surayud Chulanont, are due to hold talks on improved border security co-operation.
They will also talk about tackling the long-standing issue of dual citizenship of southern Thai Muslims, many of whom hold Malaysian passports, added Syed Hamid.
Abdullah's three-day visit to Thailand starts on Sunday.
Muslims, who are a majority in the southern provinces of Narathiwat, Yala and Pattani, often complain of being treated like second-class citizens in Buddhist-dominated Thailand, with inadequate educational and job opportunities.
They share both the religion and ethnicity of Malays, the largest ethnic group in Malaysia.
Syed Hamid also noted that the new military-backed government is more open than the elected government of Thaksin Shinawatra, who was ousted in a September coup.
Thaksin's high-handedness toward southern Thais has been blamed for fuelling separatist sentiments.
"I think Thailand now is more open... they update us with their concerns, worries, so it is a more open government,'' Syed Hamid said.
Besides offering to help Thailand improve the economy of Thailand's far south, Malaysia has said it will assist in the training of religious teachers and provide education materials on a moderate Islam.