Thailand's Malay Muslim insurgency in the south of the country appears to be going in a worrying new direction, becoming more Islamist in nature. Although the insurgency has a long history, resistance to Thai rule has waxed and waned according to local grievances. Historically, rebellion in the deep south has essentially been nationalist, not religious.

The region is the location of the former Malay Muslim sultanate of Pattani, which dates back, probably, to the 13th century when it was widely known throughout the region as a center for trade and Islamic scholarship. The primary aim of the militants was the preservation of the Malay Muslim way of life and the desire for autonomy. Although the militants have always been Muslim, it would not previously have been accurate to characterize them as Islamist or Islamic militants.

Even in the 1980s during periods of intense violence when many of the militant leaders were also Muslim scholars, the primary aim and legitimizing philosophy was the desire for national autonomy. Traditionally, religion has taken a backseat to nationalism. That began to change in 2004 with a new wave of violence, which many observers have attributed to a harsh crackdown initiated by then-Prime Minister Thaksin Shinawatra at the behest of the US administration of George W. Bush as part of the global war on terror, a now-discarded term.

In Southeast Asia, militant Islam often combined with returning Afghanistan alumni to ignite local grievances. During the 1980s, many devout Muslims travelled to aid their co-religionists in the Soviet-Afghan war. During the 1990s, often after a sabbatical in the Middle East, some of these fighters slowly filtered home to join the insurgency although it is uncertain how many returned to Thailand. A heavy-handed Thai response that included many extra-judicial killings further fuelled the reinvigorated insurgency.

The Islamization of the Malay Muslim insurgency deepened further in 2012. Buddhist monks and teachers have been regularly targeted. More than 300 schools closed recently as teachers went on strike over the worsening security situation. In September 2012, militants threatened to kill anyone not respecting Friday as the Muslim Sabbath, which forced many businesses to close and many people to remain indoors for the day.

The insurgency is now primarily a rebellion legitimized by Islam. Further complicating the nature of the rebellion are deep links to local criminal gangs, especially those centered on drug and people trafficking. Conflict in the Deep South is an extremely profitable business.

Since 2001 and the New York terror attacks, academics and specialists have probed the insurgency in southern Thailand for links to global Islamic terrorism. Nothing has been proven and the accepted wisdom is that there are no links. This view is generally accurate. There has been no grand bargain between local militants and global Islam, although the view does ignore important regional links to Islamic supporters in Malaysia and Indonesia.

However, creeping Islamization is changing the nature of this previously low-level conflict. Eventually, and regardless of the input of global Islam, the current escalation of the conflict is likely to lead to a widening of acceptable targets.

Time is running out for the Thai authorities. In December, the US Institute for Economics and Peace ranked Thailand eighth, ahead of Sudan and Israel, in a global list of 158 countries where terrorism has had the greatest impact over the past decade.i Thailand's deputy prime minister, Chalerm Yoobamrung, responded with the rather bizarre suggestion that there is no terrorism in Thailand and that the high ranking was actually a misunderstanding.ii This is despite that Deep South Watch, an independent NGO made up of journalists and academics, has estimated that the violence in southern Thailand has led to 14,890 casualties over the past nine years. Other organizations put the count considerably lower.

Thai politics continue to hamper the search for a solution. Part of the problem is that a flock of different and disparate Muslim groups, each attempting to speak for the full insurgency, makes it difficult for Thai authorities to find anybody to negotiate with. However, Bangkok, far from the region and not convinced of its importance, since it is the territory of the opposition Democrat Party, has shown no particular interest in negotiating if someone appeared to want a solution.

It is thus unlikely that the measures necessary to solve the region's problems will be agreed upon or enacted anytime soon. The conflict in southern Thailand is going to get a lot worse before it gets any better.

Current travel warnings for Thailand continue to understate the risk. While the current Australian Department of Foreign Affairs and Trade travel rating for southern Thailand is "do not travel," Thailand's overall rating is "exercise a high degree of caution" despite a specific warning of the possibility of a terrorist attack in Bangkok. Likewise, the US Department of State provides a general warning of the possibility of terrorist activity in Thailand and lists a selection of the worst recent attacks in southern Thailand, but doesn't specifically warn against travel to the region. The list includes the killing of four Malaysian tourists in 2010.

It is true that travel warnings are not a universal panacea for protecting tourists in southern Thailand, but given recent developments it would be prudent to update travel warnings to include the rest of Thailand and the northern states of peninsular Malaysia (which have often provided a safe haven for Thai insurgents).

Remarkably, the Thai insurgency has never veered near the coastal enclaves that are packed both with wealthy tourists and westerners who own beach properties in Phuket and other areas. There is precedent for caution. In 2001, an Abu Sayyaf raid kidnapped about 20 people from Dos Palmas, an expensive resort north of Puerto Princesa City on the island of Palawan in the Philippines, which had been considered completely safe.

The most valuable of the hostages were three North Americans, Martin and Gracia Burnham, a missionary couple, and Guillermo Sobero, a Peruvian-American tourist who was later beheaded. Martin Burnham was killed in a shootout between the militants and Philippine authorities a year after the kidnapping. Gracia Burnham was eventually freed.

(James Blair is a commentator on East Asian current affairs and lives in Perth, Western Australia.)