Peruvian authorities ordered Pizango's arrest on Saturday on charges of sedition for allegedly inciting violence during protests against oil and gas exploration in the western Amazon jungle.
The protests turned violent on Friday when police opened fire as they tried to break through a highway blockade manned by thousands of protesters.
Pizango accused the government of Alan Garcia, Peru's president, of "genocide" following Friday's clash.
Thousands of Indians, many armed with wooden spears, have vowed to continue their blockades on remote Amazon highways to defend their ancestral lands from outside developers.
The indigenous people hope to force congress to repeal laws that encourage foreign mining and energy companies to invest billions of dollars in projects in the rainforest.
They say that Garcia's government did not consult them in good faith before signing contracts that could affect at least 30,000 Amazon Indians across six provinces.
Al Jazeera's Teresa Bo, in the northern city of Bagua, said: "Tension is still here ... About six hours away from where we are, towards the Brazilian border, there is still a roadblock by around 3,000 indigenous protesters.
"In the city of Bagua, a curfew is still in place. The police and military are patrolling the streets.
"Some human rights organisations have arrived to investigate what really happened last Friday. They want to verify the amount of people who died. Let's remember the government says that only nine indigenous protesters died while the indigenous community says a lot more are missing.
"The government's image has come out pretty damaged by the whole situation. Not only because of the amount of people who died but also by the way they handled the situation. They tried to open up a roadblock with violence and it ended with more violence.
"We have spoken to lots of people here and they say in general, indegenous communities are peaceful people and what happened shows the anger that exists in this part of the country right now."
The bloodshed, which prompted calls for Peru's interior minister to resign, has underscored divisions between wealthy elites in Lima, Peru's capital, and poor indigenous groups in the countryside.
It has also exposed the central government's lack of control over some regions of the country.