The demonstrations started on Sunday
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Ecuador has deployed troops in an Amazon province where protesters have blocked roads and attacked one of the country's main pipelines.
The move comes after the government declared a state of emergency in Napo province, banning all demonstrations.
Three people were injured when soldiers opened fire on one group of protesters, reports say.
Activists are demanding a greater share of the profits from Ecuador's hydrocarbons exports.
They also want further investment in infrastructure and new jobs, and a crackdown on alleged corruption by big oil companies.
Ecuador's state energy company, Petroecuador, managed to resume oil exports late on Tuesday, but a privately-owned pipeline closed.
Correspondents say that other Amazon provinces are watching the protests - there are concerns that the unrest may spread.
Ecuador is the fifth-largest exporter of oil in Latin America. It produces some 530,000 barrels each day in ordinary circumstances.
Government defiant
The demonstrations started on Sunday with some activists occupying the oil pumping station at Sardinas - operated by the company OCP, which is part-owned by foreign firms.
Protesters damaged a pipeline and blocked roads in and out of the jungle province.
The defence minister accused protesters of disregard for the law
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OCP was forced to stop its operations, pumping some 160,000 barrels per day.
The suspension came hours after Petroecuador managed to resume operations. They pump about 360,000 barrels per day.
Ecuador's President Alfredo Palacio declared the state of emergency in Napo province and ordered security forces to impose calm.
Defence Minister Oswaldo Jarrin criticised the protesters, accusing them of blackmail and kidnapping.
"We will not allow anybody to damage state infrastructure," government secretary Jose Modesto Apolo told Reuters news agency.
The government indicated it would not negotiate with protesters while occupations continued, although there were signs that protest leaders were keen to talk, fearful of losing control of angry locals.
Last year, a protest in the same region stopped Ecuador's daily exports of crude oil for two weeks.