The fishermen were caught on Friday off the western Philippine island of Palawan, in waters near the South China Sea where authorities say foreign poaching of endangered or protected species has become a major problem.
"Upon initial inspection, it was found out that the said foreign fishing vessel is loaded with undetermined (number of) pieces of dead sea turtles," said Benigno Caabay, a station officer at the Palawan police provincial headquarters, quoting an official report.
The 13 are being held at a police camp in Palawan while officers look into filing a case against them, Caabay added.
In recent years, Philippine authorities have frequently caught foreigners, often Chinese, catching or buying sea turtles in the waters off Palawan.
In November last year, in the same area where the Vietnamese were caught, the Philippine navy rescued more than 100 sea turtles from poachers. But the fishermen, whom authorities believed to be Chinese, escaped.
Twelve Chinese fishermen were also arrested in April after their boat, which ran aground on a protected reef, was found to be carrying hundreds of dead pangolins, or scaley anteaters, another protected species.
The issue of foreigners poaching endangered species has become sensitive in the Philippines, with environmentalists calling for stronger action against the perpetrators.
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