"After monitoring the whale this weekend, we're delighted to see it has made its way out of Kakadu's East Alligator River and into Van Diemen Gulf," manager country and culture section, Kakadu National Park, Feach Moyle said.

Three whales entered the park in the East Alligator River a few weeks ago and one stayed, leading to fears about its safety away from the ocean.

The river is much more famous for its big crocodile population than a sanctuary for migrating whales.

"The whale made its way out on the high tides of this weekend and we're pleased it appeared to be in good condition and not suffering any ill effects," Parks Australia officials said.

"We're so grateful to Kakadu's Traditional Owners, national park staff and scientists from the NT and across the county, who have worked together to manage this very unusual situation for a good outcome."

"This is great news. It's been fantastic working with staff at Kakadu as well as expert scientists to identify ways to assist the whale, but I'm very happy it has found its own way," NT Government senior scientist Carol Palmer said.

"This is the very best outcome we could have hoped for," Dr Palmer said.