Wutthipong Wongin, a department official responsible for the eastern coast, used a photo of Wisutr Rattanasathian posted on his Facebook account as evidence for the complaint, reports the Bangkok Post.
Mr Wisutr was pictured sitting underwater on the coral reef at Koh Khram Noi in Sattahip district.
Mr Wutthipong said the man would be charged for posing a danger to an endangered species as the reef in the picture was under protection under Thai law.
The tourist could be fined up to B1 million or imprisoned for up to 10 years or both if he were found guilty.
Mr Wisutr, 45, later met with police to be formally informed of the charge. He said he had never intended to damage the reef.
The photo was taken last year and posted on his Facebook page on Saturday, he added.