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Detective Sergeant Chris Lucy said today the body was found in the Longwood Forestry block, 45km west of Invercargill.
Thirty LandSar volunteers from Southland and Otago took part in an extensive search at the forestry block last Saturday.
The 40-year-old went missing on April 16 from Otautau and had not been seen since.
"We will have a clearer understanding of the circumstances once the post-mortem has been completed, Det Sgt Chris Lucy said.
"Police wish to offer their condolences to Mr Watene's family and friends. Victim Support is working closely with Mr Watene's family and
providing them with support."
The post-mortem is set to go ahead tomorrow and a formal identification process is being undertaken.
Anyone with information in relation to this case is asked to please contact D/Sgt Chris Lucy on 03 2110400.
Alternatively, information can be passed anonymously to Crimestoppers on 0800 555 111.