The opposition said it did not like the way Mr Fernandez was detained
Bolivian President Evo Morales and opposition governors from rich eastern regions have agreed on steps to resolve the country's political crisis.
The governor of the natural gas-rich Tarija province said he would sign a deal on issues to be discussed, on behalf of other rebel governors.
They agreed to the talks despite the arrest of a northern governor.
Wealthy eastern areas have opposed Mr Morales' left-wing reforms, sparking violent anti-government protests.
Last week, Mr Morales declared a state of emergency in the northern region of Pando, where at least 16 people have been killed in anti-government protests.
Pando governor Leopoldo Fernandez was arrested on Tuesday. He is accused of hiring the hitmen who killed at least 16 farmers on their way to a pro-government rally. He denies the charge.
Mr Fernandez reportedly put up no resistance as he was transferred to Cobija airport before being taken to Bolivia's main city, La Paz, on Tuesday.
But despite the arrest, Governor Ruben Costas in the opposition stronghold of Santa Cruz said: "We have decided to sign this accord for peace to return."
The issues for discussion listed in the accord include the governors' drive for more autonomy, and talks could begin on Thursday.
Mr Morales wants to give more rights to Bolivia's indigenous community
A recent wave of violent clashes in opposition-controlled areas has left at least 30 people dead, most in Pando.
As many as 100 people are reportedly still missing after the recent violence, the scale of which prompted the president to send in troops to secure Cobija.
The violence had subsided and the blockades were lifted as the two sides began negotiations.
US black list
The unrest has centred on Mr Morales' decision to hold a referendum on a new constitution in December.
Mr Morales says he wants to re-distribute Bolivia's wealth and give a greater voice to the country's large indigenous community.
But opposition leaders oppose the plan and want to have more control over natural gas revenues in their areas.
Meanwhile, the US encouraged its citizens currently in Bolivia to leave the country, saying special flights were being made available.
President George W Bush said Bolivia had been put on a black list of nations that failed to meet obligations to limit drug production in the past year.
Relations between La Paz and Washington deteriorated sharply last week when Mr Morales expelled the US ambassador from Bolivia.