The body was found near to the waste water treatment plan which is beside the town’s golf course at about 6am on Monday.
Officers said the death is being treated as “unexplained”.
The area has been cordoned off and forensic officers are on scene.
A Police Scotland spokeswoman said: “Police in East Lothian are investigating following the discovery of a man’s body near to Haddington sewage works around 6am on Monday.
“The death is currently being treated as unexplained pending further inquiries.”