A strange S-shaped phenomenon which appeared on the weather bureau radar off the West Australian coast was caused by a military exercise, the Department of Defence has confirmed.

The shape was spotted on the weather bureau's radar map on Wednesday about 30 kilometres west off Rottnest Island.

The bureau had ruled out the phenomenon being caused by clouds.

A spokesman for the Department of Defence said in a statement on Thursday that the exercise was a regular training activity involving ships and aircraft designed to prepare a Navy warship for an operational deployment.

"The environmental conditions over the West Australian coast at the time of the activity provided a unique opportunity for this routine activity to be visible on the weather radar display," he said.

"This exercise is ongoing."

The weather bureau's Neil Bennett said on Wednesday the bureau did sometimes see shapes form on the weather radar when cloud produced a rain echo.

But nothing like the distinctive "S" shape from Wednesday.

"The radar that we use are there for the detection of precipitation, it's basically just a beam going out and hitting the rain droplets or ice particles from hail," he said.

"Sometimes the beam itself rather than going straight it gets bent back to earth and you start to pick up reflections from the ocean, rather than rain droplets."

The WA Weather Group seized on the photo on Wednesday and retweeted it to their followers.

"Nice that our pet #RottNessMonster has avoided the shark baits. Her name is Susan & she likes to eat plankton," the group tweeted.

"And I, for one, welcome our new giant sea serpent overlords," Perth Sunrise Prints tweeted.