Supporters of both sides have staged protests during the crisis
Bolivian President Evo Morales has called on opposition leaders to immediately implement an agreement to end political unrest in the country.
The deal sets out a return to order in those provinces whose governors oppose Mr Morales' left-wing reforms.
It also calls for an inquiry into the killing of 16 pro-government farmers in Pando province, which led to the arrest of the area's governor on Monday.
Eastern areas have opposed Mr Morales' policies, sparking violent protests.
The violence had subsided and some blockades were lifted as negotiations started, culminating in a pledge signed on Tuesday in which the two sides agreed to hold talks on key reforms.
Mr Morales pressed opposition leaders to begin talks on Wednesday. Issues for discussion listed in the accord include the governors' drive for more autonomy.
A recent wave of violent clashes in opposition-controlled areas has left at least 30 people dead, most in the northern region of Pando.
Mr Morales wants to give more rights to Bolivia's indigenous community
Last week, Mr Morales declared a state of emergency in the area, and its governor, Leopoldo Fernandez, was arrested on Tuesday and transported to La Paz.
He is accused of hiring the hitmen who killed farmers on their way to a pro-government rally. He denies the charge.
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 unrest has centred on Mr Morales' decision to hold a referendum on a new constitution in December.
On Wednesday, Mr Morales demanded that opposition lawmakers in Congress set a date for a referendum on a draft constitution and said the talks - which he hoped would start before the end of the day - should continue non-stop until a truce is reached, Reuters news agency reported.
US black list
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.