The Department of Fire and Emergency Services has attended dozens of call outs for storm damage in Perth's southern suburbs after a severe thunderstorm hit Rockingham.

Winds of 130 kilometres an hour were recorded on Garden Island off the coast around 10:30am on Sunday before the storm hit the mainland.

The roof was torn off a fish and chips store on the Rockingham foreshore letting in heavy rainfall which caused the restaurant's fryers to overflow.

Four fire crews raced to make it safe with the oil creating a significant fire risk.

Damaging winds brought down trees in Rockingham, Waikiki and Mardella.

Hail and torrential rainfall created localised flooding on some streets and in some homes.

The storm ripped the roof off an apartment building in Harrison Street, Rockingham. ( ABC News: Charlotte Hamlyn )

State Emergency Services crews were called to more than 16 properties Sunday morning, with dozens more call outs expected through Sunday night.

Bureau of Meteorology forecaster Adam Conroy said it was not an average thunderstorm.

"This cell is reasonably unusual in that it formed over water and was very intense and observing wind gusts of 130 kilometres per hour is very strong," he said.

"It's certainly enough to cause damage particularly to trees and that sort of thing and can also cause property damages which is what we've seen out of this."

"The thunderstorms also have reasonably low bases, which means there's a fair bit of lightning activity with it and a fair risk of that lightning hitting the ground."

That risk led Surf Life Saving WA to close a number of beaches south of Perth including Secret Harbour and San Remo.

The storm was expected to track through the south of WA through the South West and into the Great Southern.

A severe thunderstorm warning for people in the Central Wheat Belt district was cancelled about 9:40pm Sunday night.