Authorities are investigating an oil spill across a large area of Darwin Harbour that they say will be difficult to contain.

The Darwin Port received initial reports of the spill at 4:00am.

Northern Territory Environment Protection Authority (NTEPA) chair Dr Bill Freeland said the oil was believed to be a "heavy, dark fuel oil".

"If it's a fuel oil, it is either from some fuel oil storage or perhaps from a largish ship but we can't be certain as to what it is at the moment," he said.

"It is behaving oddly and it may have been contaminated with a dispersant, suggesting whoever did it may have put some dispersant in it.

"Consequently, it's formed a very thin sheen that is moving very rapidly up and around the harbour, backwards and forwards."

No effective way of containing: EPA

Dr Freeland said the way the oil had formed on the surface of the water meant it would be difficult to mitigate.

"In terms of containment, there are no really effective ways of containing fine sheens of oil spread over large areas," he said.

Authorities said the slick was difficult to contain. ( Supplied: Department of Land Resource Management )

"All you can do is perhaps break it up with propellers so you can begin to emulsify it and get it out of the water."

Dr Freeland said evidence of the oil had been found at Blaydin Point, Hudson Creek, Emery Point and also at the high-tide mark at Larrakeyah.

"So it goes from Larrakeyah all the way down to Inpex," he said. "So it is essentially contaminating a fair chunk of the harbour.

"Parks and Wildlife staff are on standby in case there are any oil birds, but we haven't found any yet."

The NTEPA has "fingerprinted" the oil so it can cross match it with another oil if a perpetrator is found.