A German woman has been found shot dead on board her yacht in the South Philippines amid fears that her partner may have been taken hostage by Islamist Abu Sayyaf militants.

Soldiers reported they found the woman naked and lying alongside a gun on the abandoned yacht. Her male sailing companion was missing.

"We are verifying reports a German national ...was taken captive by the Abu Sayyaf," army spokesman Major Filemon Tan told reporters.

He said that the al-Qaeda-linked militant group had claimed to be holding a 70-year-old German man after intercepting the yacht in Sabah, eastern Malaysia, last week.

The rebel group is known for carrying out beheadings and kidnappings and has made millions from kidnapping hostages and holding them to ransom.

There were claims that the victims could be a couple who were previously abducted by Somali pirates and held for 52 days in 2008.

In a recording claiming the kidnapping, the hostage identified himself as Jurgen Kantner, aged 70, and his companion as Sabine, according to Mr Tan.

Photos apparently taken at the scene also identify the yacht as their boat the Rockall, according to AFP.

Abu Sayyaf hostages Robert Hall and Kjartan Sekkingsta in a picture released by the rebels. Credit: Reuters

Abu Sayyaf rebels have been intercepting slow-moving tug boats since March and taking soldiers Indonesian and Malaysian soldiers.

Several hostages had been freed, after paying ransom to the Abu Sayyaf, including two Canadians this year.

It is holding 15 captives, including a Netherlands citizen, five Malaysians, two Indonesians and seven Filipinos.