Police said the 68-year-old man was arrested at a home in Fortitude Valley about 7pm in relation to alleged drug offences and taken to the Brisbane City Watch House.
Shortly after arriving in Brisbane, police said the man was found unresponsive in the police vehicle about 7.17pm.
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Officers gave the man first aid and paramedics attended the scene, but he couldn’t be revived, police said.
The Ethical Standards Command is investigating his death and a report will be prepared for the coroner.