The 67-year-old was swimming at Wangi Falls in Litchfield National Park about 11.30am local time on Monday when the reptile struck.
He is understood to have non-life threatening injuries to his arm and back.
The man was initially treated at Batchelor medical clinic before being transferred to Royal Darwin Hospital, where he remains in a stable condition.
The NT Department of Environment, Parks and Water Security closed the popular tourist spot after the incident.
"It is estimated the crocodile is approximately two metres long," the department's head of Northern Australian Parks, Dean McAdam, said in a statement.
"Rangers are working with the Crocodile Management Team to remove the animal.
"Further crocodile surveys will then be undertaken prior to reopening."
A holidaying police officer helped the man following the attack, with Senior Constable Taneka Starr in the water at the time with her family and later describing the incident as terrifying.
"My family and children were swimming in the water when people started yelling for everyone to get out," the detective said in a message posted on Tasmania Police's Facebook page.
"We formed a circle together to make sure we all made it out of the water safely as a group, especially the children.
"We then saw that a man had suffered injuries to his arm and together my sisters and I provided first aid."
Litchfield National Park is about 115 kilometres south of Darwin. Wangi Falls is a large shaded waterhole that flows all year.
It is closed during the wet season when saltwater crocodiles can move up flooded rivers.
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