Thieves in Darwin's rural area may have received a nasty surprise if the crocodile trap they were stealing had one of the predators inside.

Rangers are mystified by the bizarre incident, which likely saw perpetrators wading through croc-infested waters before making off with the unwieldy device.

The three-metre trap is part of the Government's crocodile management program and is regularly checked and re-baited.

But when rangers returned to check it last Sunday, the trap was missing.

Senior crocodile ranger Tom Nichols said it was likely stolen then dragged through bushland and private property some time in the preceding two days.

"The trap was set on pontoons in the water itself, so they would've had to enter the water and drag that particular trap out," he told ABC Radio Darwin's Jolene Laverty.

"It wasn't something which was just random. We believe that, obviously, someone intending to steal this trap has put a fair bit of effort into it.

"This was a pretty low act, and one thing we have the traps there for is public safety as there's a large number of crocs in that area, especially in the wet season."

Croc may have been inside trap when stolen

A 2.4-metre crocodile was removed from the location last month.

Crocodiles had also been sighted in the area in the days beforehand and Mr Nichols said he suspected there was one in the trap.

"The bloke who checks that particular area, he saw a croc the night before and he believes it went in there," he said.

"Even the way they dragged it out, it just looked like a crocodile was in it; I can't guarantee it though."

Further bewildering the rangers is why the thieves might want the trap.

"This is probably the second time it's happened," Mr Nichols said.

"A lot of people utilise that area, especially kids, and it means we're going to have to put another one in, and these things cost a fair bit of money."

People found guilty of interfering with crocodile traps risk a maximum penalty of $7,750 or six months' imprisonment.

The potential penalty if traps have crocodiles in them is heftier at $77,000 and five years' imprisonment.