The men disposed of the bodies of Japanese businessman Yuji Okada and his girlfriend in early July on the orders of a Filipino suspect who remains at large, the department's National Bureau of Investigation said.
The men initially buried the bodies on a sandy riverbank east of Manila, but later dug them up after a stray dog disturbed the site, said senior investigator Joel Tovera.
"They loaded the bodies on a boat and sailed to Polillo island, where the by then bloated bodies were strapped to sandbags and dropped into the water," he told a news conference.
The Japanese embassy in Manila could not be reached for comment late today.
The grisly confessions came a day after the South Korean embassy in Manila expressed alarm at a rise in crimes against its nationals in the Philippines, citing the killing of nine South Koreans this year alone.
Tovera said the authorities are looking for a total of four Filipino suspects, in addition to those already arrested over the couple's disappearance.
The couple were apparently killed by a Filipino man and his Filipina girlfriend at Okada's suburban Manila home on June 28 after an unspecified argument with Okada's girlfriend, Tovera said.
Tovera said the three men who confessed to dumping the bodies at sea were pricked by conscience.
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