Two buildings, poor weather and a low-flying aircraft created the illusion that a light plane had crashed into mangroves near Darwin Harbour overnight, police say.

Several witnesses told police they had seen a light plane end up in bushes just after 6pm, sparking a large-scale search involving the CareFlight helicopter and land-based police.

"[We had] seen a plane balancing on top of the mangroves," a witness was quoted as saying in the NT News.

"It was a small five-seater plane that was balancing."

The search was called off early this morning after no sign of the missing aircraft was found.

Duty Superintendent Mike Murphy said two buildings, bad weather and the close proximity of Darwin airport's flight path combined to create the illusion.

"Given the environmental factors, the rainfall, the low light, mate, it would be easy to misinterpret it as a light aircraft," he said.

"I've actually seen it myself.

"It's remarkable how it looks like a light aircraft pointing out into the ocean."

He said the witnesses did the right thing by alerting emergency services to a potential accident.