Scuffles between police and protesters broke out following a sit-in outside the Queensland Police headquarters on Friday.

Protesters spilled across Brisbane's CBD as police struggled to control the demonstration over the woman's death.

Police are investigating the death, but say an autopsy indicates the 49-year-old died from natural causes.

The woman appeared in court on Monday on drug and property offences and was remanded in custody until October 7.

She had been due to be transferred to prison from the Brisbane City Watch House but was found dead in her cell early on Thursday.

It is the first time anyone has died inside the station in its 20-year history, Assistant Brisbane Commissioner Brian Codd says.

"I'd like to sincerely pass on my condolences to her family, her loved ones, her next of kin, and also particularly the elders of Indigenous communities who we've been engaged with throughout yesterday to assist in, I guess, respecting the cultural sensitivities associated with her passing," he said on Friday

"A post-mortem examination appears to indicate that the death was by natural causes."

The Ethical Standards Command is investigating her death on behalf of the coroner, overseen by the Corruption and Crime Commission.

Protesters rallied outside the Roma Street headquarters early on Friday, chanting "let them go" as officers handcuffed a protester and put them in a police van.

After scuffles broke out with police, the demonstrators moved through the city, disrupting traffic, before coming to a halt at the Queen Street mall just before noon.

Brisbane councillor Jonathan Sri, who filmed the event, said the demonstration was peaceful until officers became involved.

"Residents were protesting peacefully, spaced out safely, and without warning or negotiation police started arresting people, turning a safe situation into a tense one," Mr Sri said.

Footage showed demonstrators gathered around a police vehicle while some painted their hands red, chanting "blood on your hands" at officers as what looked like handprints were smeared on the walls of the police headquarters and on waiting vehicles.

Mr Codd said there were significant and sensitive issues relating to the incarceration rates and deaths in custody of Indigenous people which were "worthy of debate".

"What is more difficult to sustain, however, is when groups of people utilise or use for their own particular benefits a tragedy such as the death that we experienced yesterday."

He said what might have been an acceptable public demonstration six months ago was no longer appropriate during the COVID-19 pandemic.

Australian Associated Press