The whale and others were on an annual sea migration when some of them "took a wrong turn", experts believe.
Two whales were later able to swim out of the river, but at least one remains.
It's the first known instance of a whale being found in crocodile territory so far inland in Australia.
Given its estimated 16m (52 ft) length, the humpback is considered unlikely to be disturbed by crocodiles.
But that risk could escalate if the whale were to become stranded in the shallow waters, officials said on Monday.
Wait, what happened?
The whales were spotted last week in the East Alligator River by people boating in the Kakadu National Park - Australia's biggest national park and a World Heritage-listed site.
The sight of the animals swimming along the muddy bends of the river - so far from open water - has amazed locals.
"It's something that's never been recorded before - not just in the Northern Territory - but [in] Australia. It's really, really unusual," said Carole Palmer, a marine ecosystems scientist for the territory's government.
It was hard to determine if more than one whale needed assistance because of the river's "murky brown water", she added.
How did the whales get there?
Ms Palmer told the Australian Broadcasting Corporation that experts weren't sure "why these whales took a wrong turn" off the country's north coast.
It is thought they had been heading south to Antarctica but mistakenly entered an estuary which took them further upstream into the river system.
Whales migrate to warmer waters off Australia during spring to give birth before heading back to Antarctica to feed.
Is there danger?
Although the river teems with saltwater crocodiles, experts do not expect a confrontation.
But if the whale becomes trapped in the shallow bends and washes up on a bank "it's an easy feed for them," Ms Palmer told the ABC.
"There's no way we can lift a 12-16m humpback whale off the sandbar and that's potentially when the crocs would kick in."
What are officials doing to help?
To clear a path to the ocean, boats have been banned along part of the river.
It had been hoped the whale would leave on its own, but it has remained around the deepest section of the river - about 20km from sea.
Ms Palmer said officials were considering several options to draw it out, such as using "noisy sound" from nearby boats or recordings of humpback whale calls.
"It's tricky on every level, but everyone is really trying to move forward with this in the most positive way that we can," she said.
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