An outdoor party for a 30-year-old man on Saturday turned into a tragedy when a crocodile attacked and ate one of his guest, a 24-year-old man from Darwin while they swimming across the muddy river.

The incident happened at the Mary River Wilderness Retreat, which is halfway between Darwin and the Kakadu National Park at around 3 pm.

Two party guests were swimming on the river when a five-metre long saltwater crocodile grabbed one of them.

Geoff Bahnert, watch commander of the retreat, cited witness account of the incident in which the victim was taken in the jaw of the reptile for a long period and then became out of sight, presumably eaten by the croc.

He warned visitors to the retreat that the river is known to have the greatest saturation of adult saltwater crocs in the world. There had been other similar incidents in the past. In December 2012, a 9-year-old boy was attached by a croc near Dhania, while in November 20012, a 7-year-old-girl was eaten by another croc at Gumarrirngbang outstation.

He opined the victim could have taken some alcohol which led to his dip on the river.

When the police and Northern Territory Crocodile Management Team arrived at the park, one of the officers shot the largest croc in the area, but it is unknown if that was the same reptile that attacked the male partygoer.

Mr Bahnert said the action was necessary so the reptiles would not hamper search and rescue operations since crocodiles are known to be territorial.

The victim's family has been informed of the accident and they drive to the site from Katherine and were given a briefing by police on recovery operations.

Since it has been 20 hours since the victims has been missing, the searchers "hold the gravest of fears" that the man is dead, he said.

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