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 indigenous people, many armed with wooden spears, have vowed to continue their blockades on remote Amazon highways to defend their ancestral lands from developers.
Peru's indigenous peoples 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 indigenous people across six provinces.