Juan del Granado, of the social democratic Movement Without Fear, told reporters President Evo Morales and Vice President Alvaro Garcia, who apologized but denied ever giving any orders for the repression, actually were to blame.
"The officials directly behind the repression order, the plan, and carrying it out, were Evo Morales y Alvaro Garcia Linera," charged del Granado. Police fired teargas and 74 people were injured in the September 25 crackdown, according to official figures.
Morales is the country's first elected indigenous president and came to power on a wave of indigenous support. He and former interior minister Sacha Llorenti, who later resigned, denied ordering the crackdown. The defense minister and migration chief also resigned.
After a year-long investigation, justice officials ordered the arrest of the police chief and said Llorenti was not to blame. He has just been named Bolivia's ambassador to the United Nations.
The national Ombudsman's Office in 2011 identified 18 people it said were responsible for the repression, but it did not name Morales or Garcia.
Morales, a socialist coca leaf growers' union leader, has argued that the 300-kilometer (185-mile) Brazil-financed highway is vital for the country's economic development. Bolivia is South America's poorest nation.