Defence Minister Chetta Thanajaro told reporters on Monday the government had already made "official-level contact" with Wan Kadir Che Man, the leader of Bersatu, an umbrella organisation of three separatist groups.
"If the leader wishes to talk, we are ready to talk. Don't forget that he is a Thai national," Chetta said.
Meanwhile, Wan Kadir was quoted by The Nation newspaper as saying he was willing to give up a century-old demand for a separate homeland in the south, the only Muslim-majority area in the predominantly Buddhist Thailand.
Wan Kadir's reported willingness to talk about autonomy rather than a separate homeland could be a major step in ending the spate of violence in the Muslim south that has left more than 200 people dead this year alone.
"This is the age of globalisation. The world has moved on and there is no more room for separatism," Wan Kadir was quoted as saying by The Nation.
Reconciliation could come about only if Thailand's minority Muslims are given more "political space" and have a bigger say in the development of the south, Wan Kadir was quoted as saying.
Thai Muslims, who are linguistically and culturally closer to Malays of Malaysia, complain the government does not recognise their Islamic Malay culture, tries to suppress their language and discriminates against them in jobs and education.
In comments on Monday to the British Broadcasting Corporation's Thai language service, Wan Kadir said he was ready to talk with the Thai government, but did not confirm Chetta's claim that contacts have already been made.
More than 100 people were killed
during clashes in April
"They are trying their best ... so we should sit and talk," he said, speaking in Thai on the BBC programme monitored in Bangkok.
Wan Kadir spoke about the cultural chasm between the Buddhists and Muslims of Thailand.
"It is not that the Thai government does not want to resolve the problem, but they do not understand me, they do not understand us. I am a Malay Thai," Wan said.
The separatist insurgency simmering for decades in the provinces of Yala, Narathiwat and Pattani turned violent a few years ago. It gathered pace this year with almost daily killings by unidentified gunmen of about 100 Buddhist officials, policemen and clergy.
The killings tapered off after 28 April when security forces killed 107 alleged fighters who had tried to storm 10 security outposts in coordinated attacks.
"It is not that the Thai government does not want to resolve the problem, but they do not understand me, they do not understand us. I am a Malay Thai"
Wan Kadir Che Man,
leader of Bersatu group
"Several hundreds of our group were murdered ... and people have questioned us," Wan Kadir said on BBC in a tacit acknowledgment that his group was behind the 28 April raids.
"They asked Bersatu and other factions: 'What are you going do when hundreds of Muslim are being murdered? You have to find the answer to our question.' People are still angry ... Bersatu is trying to find a solution," he was quoted as saying.
Wan Kadir, who had studied in the US, went into exile in Malaysia nearly 15 years ago after Thai authorities accused him of being a member of a separatist group, the Pattani United Liberation Organisation.