The reported tornado, or water spout triggered a scaffolding collapse on the Orsino Boulevard worksite, which is only about 100m from the ocean in the southern Perth suburb.
The incident, which saw a total of 10 people injured, was reported at about 2.15pm yesterday.
Cockburn District firefighting chief Tony Nicholas described the occurrence as "an unusual event".
"We were called to a structural collapse of scaffolding due to swirling wind conditions, possibly a mini tornado," he said.
"We received a call suggesting there were personnel from a construction company at were injured in that collapse.
"Initial crews were from St Johns and police followed by crews from Fremantle fire station. They have advised me people were a number of casualties treated for minor to significant injuries."
Mr Nicholas said there was no one trapped in the incident and the scaffolding was designed to hold concrete, but there was no concrete on the platforms at the time.
"The workers advised they saw some strong winds coming off the ocean, there was some photos taken of those, the Bureau of Meteorology is here on site they will be conducting some investigations," he said.
"We have wind speed specialists and they'll be working with WorkSafe to try and prevent it from happening in the future."
No workers were hit by the scaffolding, but some did fall with the scaffolding about three metres.
There are also reports the crane operator took evasive action to prevent the crane on site from swinging in to the wind, but Mr Nicholas could not confirm those reports. Private security will now remain on site for the rest of the night.
Bureau of Meteorology spokesman Neill Bennett said BOM had also received reports of the tornado and confirmed weather conditions on the coast could have created the water spout.n“They are very, very localised events and we do see them off the coast,” he said. However he said there were difficult to predict and sometimes cannot be seen on radar images.
Two people were taken by ambulance to Royal Perth Hospital with suspected head and spinal injuries.
The other three workers were sent to Fremantle Hospital with minor injuries. Two were discharged overnight, but a third remains in hospital in a stable condition.