Petroecuador issued a statement saying pumping resumed at 9:15 a.m. (1415 GMT) through the Trans-Ecuador pipeline and it said the flow should be back to normal within hours. Closure of the line had forced Petroecuador to accelerate three 360,000-barrel shipments of oil for China to free storage space.
A rain-caused landslide on Friday ripped up a 100-meter (100-yard) long stretch of the line near the Reventador volcano.
The company said it did not know how much of the 420,000 gallons (1.6 million liters) of crude oil that spilled had reached the Quijos river, a waterway popular with whitewater rafting enthusiasts.
But enough flowed from the Quijos into the Coca and Napo rivers downstream that the regional capital of Coca had to shut down its drinking water system and Ecuador's government alerted Peru and Brazil, which are along the course of the Napo as it heads toward the Amazon.
In Coca, an urban area of about 80,000 people at the confluence of the Coca and Napo rivers, Mayor Ana Rivas told the Sonorama radio station that the accident "has left us without water because the river we take potable water from is contaminated. The people are indignant because there is no water to drink."
Petroecuador has distributed bottled water to the city and Rivas said officials were using tankers to collect water from an uncontaminated stretch of river.
Alexandra Almeida of the environmental group Accion Ecologica expressed concern because "they still don't know the real quantity of this spill of crude that affected the principle sources of water of this region."