The Rev. Douglas Leslie Rowe, 69, was found dead in the village called Can-asuhan in Carcar City, around 25 miles south of Cebu City, The Manila Times reported. He had been inspecting a parcel of land with two Filipino female companions.
Police said Rowe's companions -- Jan Rebutaso, a nun, and local real estate broker Sunshine Hoyo -- went off to take pictures of the land and left Rowe near the river at his request.
When the women returned they saw the Jesuit priest's body in the river, the Times' report said.
"His undergarments were below his knees," a police officer told the newspaper. "The two women rushed Rowe to hospital but doctors pronounced him dead on arrival," the officer said.
Police said they are keeping an open mind about the death of Rowe, who was from Midland, a suburb in Perth in Western Australia, until they get a forensic report.
But police said the women claimed the priest suffered from heart disease, was hypertensive and diabetic. He "could have suffered a heart attack or stroke while relieving in the river. We still don't know. There is an ongoing investigation," police officer Vicente Garcesa said.
Rowe was the founder of the Patrist Society of the Sons and Daughters of God the Father, based in Australia and had put up churches in Cebu City and in Meru in Kenya -- the two countries where the group had missions.
Rowe had specialized conducting retreats for nuns, priests and bishops for several years and was an author of several religious books, the official Web site of the order says.
He was also an accomplished jazz and classical musician.
In the Philippines every week the order feeds poor children "who have no proper home, no proper parents and probably no future," the Web site says.
"We also house children who have home related problems. We teach children and adults about God and about prayer."
Cebu City is about 360 miles south of Manila and regarded as the seat of Christianity in the Philippines because Western explorers, including Ferdinand Magellan, landed on the island's shores.
Missionary priests have been the target of rebel kidnappers in the Philippines but mainly south of Cebu on the island of Mindanao, a more heavily Islamic and also rebellious area.
Between 120,000 and 150,000 people are estimated to have been killed in the struggle between government troops and rebel groups seeking an independent Mindanao region.
One rebel group is the Moro Islamic Liberation Front. But the MILF also has had peace agreements with the central government and has actively helped free kidnapped people, including priests.
In November 2009, the MILF helped behind the scenes to free the Rev. Michael Sinnott, a Catholic priest. The MILF leadership negotiated with disaffected rebel factions who were holding Sinnott hostage to hand him hand over.
Sinnott was walking in his garden the month before when men stormed his residence and hustled him into a waiting van that later was found abandoned along the coast. Fears for his health mounted during his abduction because he required medication as a result from a heart bypass operation.
Sinnott, 79, and a native of Wexford, Ireland, was ordained in 1954 with the Missionary Society of St. Columban, an order that has been working with the poor of the Philippines since 1929.
Despite the good work done by the Columbans, the order suffered a kidnapping in August 2001 that resulted in the death of the Rev. Rufus Halley, who was killed by his abductors.