Divers braved waters where a crocodile was spotted to search the area where the body was last seen in Darwin Harbour about 6.30pm on Sunday.
Police arrived only to see the body submerge under water, Chris Harden, acting officer in charge of the Northern Territory Police search and rescue section, told reporters on Tuesday.
Air, water and ground teams searched for the body for three days, including the use of a helicopter and jet skis, and assisted by NT Surf Life Saving members.
Police divers were deployed on Tuesday but found no trace of the man.
A crocodile management team was on hand as a precaution after a helicopter's crew sighted a croc in the area.
Police on Wednesday said they had suspended the search but would continue inquiries.
They want information from anyone who might hold concerns for a person who has failed to attend appointments or has been uncontactable, particularly in the Darwin Harbour area.
The man is described as Caucasian, with a slim build and medium-length grey hair, last seen wearing a light-coloured shirt.
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