Mr Fernandez supported an autonomy referendum earlier in 2008
Bolivian troops have arrested the governor of a northern province wracked by deadly anti-government violence in recent days, state television reports.
Leopoldo Fernandez, an opponent of President Evo Morales, is accused of backing violence in Pando in which some 16 people died.
Mr Morales declared a state of emergency in Pando last weekend.
The region is among several demanding autonomy and opposing Mr Morales's plans for constitutional reform.
Government troops who took control of the state capital of Pando, Cobija, moved to detain the governor on Tuesday, according to reports.
Mr Fernandez put up no resistance as he was transferred to Cobija aiport, from where he would be taken to Bolivia's main city, La Paz, the Efe news agency reported.
Pando is a remote northern region of Bolivia situated in the Amazon basin on the borders with Peru and Brazil.
Mr Morales' central government accuses the regional government, headed by Mr Fernandez, of inciting civil unrest in the region.
The fighting led to a string of violent deaths and the disappearance of about 100 people, Efe says, prompting the president to send in troops to secure Cobija.
The arrest came as opponents of the president Bolivia appeared to be nearing a truce with Mr Morales that could end ongoing violence.
The governor of Tarija, in the south of Bolivia, said he expected to sign a deal with the president on Tuesday, Reuters reported.
On Monday, the leaders of nine South American nations backed Mr Morales at an emergency summit in Chile.
Mr Morales has likened the unrest in opposition-controlled regions of his country to an attempted coup.
But the unrest, in which protesters have blocked roads and occupied public buildings, represents the most serious challenge to Mr Morales since he took office almost three years ago