LATEST UPDATE: Crocodile experts say the Mary River pair may have been breeding prior to the capture of the 3.1m female overnight.
The saltwater crocodile was harpooned by rangers on a boat patrol and Environment Minister Andrew Powell said it was quite an operation to catch the reptile.
"This croc has been very wary of our rangers on the river for many months now," he said.
"It surfaced about a metre away from one of our boats at about 2am and (rangers) were able to fire a non-lethal harpoon and then wrap it up in a piece of rope and actually swim it in to a boat ramp.
"Between my rangers and some very helpful police officers, they were able to remove it from the water and have it ready to transport to a croc farm in Rockhampton in central Queensland."
This croc was first spotted by fishermen in July, but the Queensland Parks and Wildlife Service has been patrolling the river since May, 2012, when the first 3.5m crocodile was sighted.
Mr Powell said despite the capture, residents should remain vigilant with the larger saltie still lurking.
"People do need to be croc-wise around the Mary River," he said.
"The one remaining is even larger again and people need to be very careful around boat ramps and fishing."
UPDATE: Environment Minister has confirmed a crocodile has been captured overnight in the Mary River.
Minister for Environment Andrew Powell will be at Tinana at 2pm to talk about the capture.
EARLIER: The long hunt to catch one of the Mary River crocs may be over, with a Maryborough man claiming he spoke to rangers who told him one of the reptiles had been captured.
Chicka Derwent goes for a walk by the Mary River each morning and on Thursday he noticed Queensland Parks and Wildlife rangers near the Lamington Bridge in a four wheel-drive with a trailer tying something down.
He approached the rangers and asked how the hunt for the crocodiles was going and one of the rangers replied that they had caught one.
The rangers told him they had harpooned the crocodile, an action that would not have harmed the reptile as its hide was only penetrated by a few centimetres, Mr Derwent said.
He said he was told the crocodile was about 11 feet long and was being moved to a secret location.
"They caught it up the river," Mr Derwent said.
He said some men fishing off the floating pontoon had helped the rangers move the crocodile after it was caught.
Two crocodiles have previously been sighted in the river.
The Chronicle is seeking comment from the Department of Environment.
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