Three Humpback whales were sighted in the East Alligator River earlier last week although only one was spotted later in the week.

"As far as we're aware, this is the first time this has happened," Parks Australia staff said.

Kakadu National Park staff are monitoring the situation and working with NT government authorities to gather data on this unusual event, an expert working group has been set up to monitor the whale and prepare plans for intervention if required.

There is an exclusion zone in place from the mouth of the East Alligator River to a point approximately 30kms upstream for the welfare of the remaining whale and for the safety of people who may have been considering going to the area by boat.

"The last thing we want is a collision between a boat and whale in waters where crocodiles are prevalent and visibility underwater is zero. We also don't want boats to inadvertently force the whale further up the river," a parks spokesman said.

"The whale is not in distress at the moment and it is not an emergency situation. The best case scenario is for the whale to make its way back out to sea. Kakadu National Park and NT Government scientists will continue to monitor the whale in the coming days.

"We appreciate that this is a very unusual and exciting event, however, our priority at present is to ensure the safety and wellbeing of visitors and the whale."

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