The Philippine-flagged MT Terranova went down with 1.4 million litres of industrial fuel oil on July 25 in rough seas churned by Typhoon Gaemi, killing one crew member.
The coast guard had warned that if the fuel had leaked it could have caused the country's biggest oil spill and an "environmental catastrophe".
"The salvor informed us that we have recovered 96 percent of the oil waste," Lieutenant Commander John Encina said in video comments shared with the press by the Philippine Coast Guard.
"What we're getting now is mostly water."
Government agencies involved in the undertaking decided at a meeting Thursday to announce on Friday the "conclusion of the syphoning operations", said Encina, who is supervising the effort.
Some 1.38 million litres of oily waste were retrieved between August 19 and September 10, the coast guard said earlier.
The mixture of oil and water was taken to a treatment facility near Manila.
The coast guard earlier said the oil that escaped from the vessel's tanks had been minimal, but local governments imposed "no-catch" zones affecting tens of thousands of fishermen in the bay.
The government plans to refloat the ship for an ongoing enquiry into the sinking.
Encina declined to discuss the investigation on Thursday.
One of the worst oil spills in Philippine history occurred in February 2023, when a tanker carrying 800,000 litres of industrial fuel oil sank off the central island of Mindoro.
Diesel fuel and thick oil from that vessel contaminated the waters and beaches along the coast of Oriental Mindoro province, devastating the fishing and tourism industries.
The oil dispersed over hundreds of kilometres of waters famed for having some of the most diverse marine life in the world.
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