Experts had feared the weight of the water could have breached the crater walls and flooded the homes of up to 40,000 people in and around the small coastal town of Botolan.
Greeted with relief
But on Friday officials announced the danger was over.
"We have ordered everybody to go home," said provincial Governor Vicente Magsaysay.
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He said the government had provided buses to take back the 9,000 people who had heeded the official evacuation warnings. Some villagers had been allowed to go home on Thursday.
Residents greeted the news with relief.
"We no longer have food," said one man, Luis Benito. "Food distributed in the evacuation centre was not enough."
Huge task
It took workers several weeks digging with picks and shovels to complete the five-metre-deep drainage channel leading into the River Bucao.
It is believed this is the first time such an operation has been carried out anywhere in the world.
"It's a good success story... it's something we can be proud of," vulcanology institute chief Raymundo Punongbayan told local television. "There was zero damage to people or property."
The problem has its roots in Mount Pinatubo's 1991 eruption, when 800 people were killed.
The volcano's top was blown off during the eruption, leaving a hole covering five square kilometres (two square miles).
Over years the crater filled with rainwater and scientists decided to drain it after the waters rose to critical levels following weeks of monsoon rains.
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