A crime scene was declared in Woombye, north of Brisbane, after an accident on the Sunshine Motorway.
One of the vehicles involved fled the scene and was tracked north by police.
A man allegedly stopped the vehicle and approached officers while armed with a gun before he was shot.
First aid was administered before the man was taken to Sunshine Coast University Hospital in a stable condition.
The incident would be investigated by the Ethical Standards Command with oversight by the Crime and Corruption Commission, police said.
It comes after two people died and another was injured in separate incidents involving police on Tuesday.
Police responding to a welfare check request shot dead a man in his Tingalpa home in Brisbane's east.
Officers had tried to negotiate with the 21-year-old man after he was alleged to have threatened officers with a knife.
The incident is also being investigated with oversight from Queensland's Crime and Corruption Commission.
In a separate incident in Sydney, another man was shot dead after he was alleged to have assaulted two women at a unit complex in inner-city Potts Point.
The man was identified by media outlets on Wednesday as celebrity dentist Steven Lin.
In a third incident, police from the high-risk domestic violence offender squad shot a man in Newcastle.
Two stun guns were deployed against the man, but were ineffective.Â
The man was taken to hospital in a stable condition.
Both NSW incidents are being investigated by out-of-area police before being reviewed by the internal police investigative unit.
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