Thailand's cabinet has approved plans to re-organise the military command structure in its strife-torn south.
Mr Thaksin has faced criticism of his handling of the insurgency
Sirichai Thanyasiri, the general in charge of fighting a Muslim insurgency, has been recalled to Bangkok, with a new committee installed in the region.
Prime Minister Thaksin Shinawatra has promised a newly aggressive approach, arresting those suspected of violence and building links with local people.
Over 600 people have died in the mainly Muslim south since January 2004.
A government spokesman, Chalermdet Chompoonut, said the reshuffle aimed to "eradicate conditions that cause unrest, conditions that leave people feeling alienated and unequal".
The new committee, to include Thailand's interior minister as well as civilian, military and police officials, would aim to convince militants to change their ideology and accept peaceful co-existence, he added.
Home to most of Thailand's 4% Muslim minority
Muslim rebels fought the government up to the mid-80s
Suspected militants have upped attacks this year, targeting Buddhists
Security forces' response criticised by rights groups
Gen Sirichai, who has been in charge of a special border unit since it was created in October 2004, is to be posted to a new position under the control of the prime minister's office.
The army commander for 14 southern provinces will take over direct control of the unstable region close to the border with Malaysia.
The re-organisation comes amid a constant stream of attacks in the region, where the Thai government has been accused of failing to reduce the level of violence.
Mr Thaksin was re-elected in February pledging to inject new life into peace moves, and recently inaugurated a National Reconciliation Commission.