The villa, accessible only by sea or a footpath, is close to the superb Trisara Resort, one of the 10 properties under investigation.
The Department of National Parks, Wildlife and Plant Conservation has appointed 10 teams - all from outside Phuket - to investigate the 10 properties.
A Frenchman is currently renting the newly-discovered villa on a 30-year contract, according to Trisara investigator Sermyod Sommun, the Director of Conservation Operation Region 16 (Chiang Mai).
The property also has a pier, for which there appears to be no paperwork, he said.
How officials failed to spot a pier that allegedly is not supposed to be there opens another range of questions.
Khun Sermyod aims to pursue the owner of the land and the bureaucrats who awarded the title.
He said a Sor Kor title for 20 rai in the region appears to have mystifyingly grown to include 200 rai.
Most countries have standard land titles but the mutiple titles available in Thailand have helped to create the potential for deceit.
''Flying'' Sor Kor titles - issued for one section of land then transferred to cover another - are likely to complicate the pursuit of the culprits in the Sirinath National Park cases.
The resort owners involved deny any wrongdoing.
Phuket's property industry relies on the certainty of ownership and one consequence of the current investigations may be greater due diligence and larger fees for lawyers.