Its Facebook page erupted with criticism over why locals weren't told about the storm until five minutes after it hit the inner city.
Winds up to 90 kilometres per hour lashed the bayside, small hailstones fell all over the city, four centimetres of rain was dumped on the CBD in just half an hour, and 10,000 lightning strikes tore through the sky.
Cars were submerged in the inner-city suburb of Bowen Hills and trees toppled over throughout the city.
The BoM said the storm showed signs of severity only when it approached Brisbane.
For a warning to be issued, a storm must meet certain rain, wind, hail and tornado criteria, and the storm on Saturday had only ticked a couple of those boxes, when it was too late, the BoM said.
"The short duration - from minutes, and often less than and hour - and very localised nature of thunderstorms make them very difficult to predict in nature," the BoM's Queensland regional director Rob Webb said.
"The bureau ... doesn't aim to issue warning for every thunderstorm but uses thresholds to ensure there isn't complacency in the community due to over-warning," Mr Webb said.
Locals are unforgiving and have taken to social media to take aim.
"BOM your letting those who trust you will inform them DOWN!!!," David Cook posted.
"Got caught with your pants down on that one hey BOM???," Jess Lyn posted.
Ipswich councillor Paul Tully also went public with his criticism, accusing the bureau of being asleep on the job and calling for an apology and an internal inquiry for its "monumental failure".
"They must have been enjoying a long morning tea or an early lunch not to realise the intensity of the approaching storm," Mr Tully said.
About 2500 people in southeast Queensland are still without power.
-AAP
