Lukman wrote: "The worst-case scenario can still be avoided, but only if Mr Samak and the military forces allow the people of Pattani to determine their own future.
"If, in a referendum sanctioned by Bangkok, Pattani chooses independence, there will be one less border in the world marked by endemic conflict."
More than 2,900 people have died since violence flared in 2004. Drive-by shootings and small-scale bombings occur almost daily.
Four small bombs exploded in the region on Friday, which authorities blamed on the separatist forces.
One of the blasts wounded three people at Yala's Rajaphat University, police said. The groups often target public schools and other buildings associated with the government.
Three other small bombs went off in different parts of Narathiwat. No casualties were reported.
Lukman's organisation, known by the acronym Pulo, is one of several groups involved in a century-old struggle for independence in the south.
It was not clear to what extent Lukman's comments reflected the views of the other shadowy groups involved.
Thailand annexed the independent sultanate of Pattani in the early 20th century, and the mostly Muslim region is now divided into three provinces, Pattani, Narathiwat and Yala.
Residents have long complained of being treated as second-class citizens.
Past governments have failed to quell the insurgency despite the presence of 40,000 troops and police officers in the region.