The Terrace Hotel on St George's Terrace was opened with great fanfare earlier this month in a restored heritage building offering 15 luxury rooms at a cost of nearly $500 per night.
The unseasonal storm that swept through the city lifted off the hotel's roof lining and dislodged a chimney, sending rubble onto a pedestrian walkway below.
Police and emergency services were quickly on hand to cordon off the area, as glass and brick continued to fall on the street below.
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Fallen trees were also causing traffic chaos in the city centre and Kings Park, and around 16,000 customers in the metropolitan were left without power due to bad weather.
The Department of Fire and Emergency services were warning residents of dangerous thunderstorms - featuring damaging winds, large hailstones and heavy rain - headed for Esperance, Norseman, Laverton, Warburton and Eucla.
Surf Lifesaving WA closed Cottelsoe Beach because of dangerous conditions, and two boats were blown ashore in Bunbury.
Western Power later said more than 27,000 customers had lost power during the storm, with outages affecting people in Balcatta, North Beach-Karrinyup, Bibra Lake, Yokine, Wanneroo, Kalamunda, Wangara and South Bullsbrook in the metropolitan area.
The power supplier said strong winds had flung debris and branches into powerlines, with more than 55 hazards reported on the network.
The storm also caused damage to parts of the regional network, with customers in Australind, Dandaragan and Narrogin experiencing outages on Tuesday night and Wednesday.

