The deaths of two Indigenous men who died in the Townsville flood waters is being treated as "deaths in custody".

The bodies of the men, aged 21 and 23, were found in a drain near Aitkenvale Park on Tuesday afternoon after floodwaters receded.



The discovery followed a search operation after the men had been spotted near flood waters on Ross River Road.

Shane Duffy, CEO of the Aboriginal and Torres Strait Islander Legal Service (ATSILS), confirmed the deaths will be investigated.

"ATSILS has confirmed with the State Coroner’s Office that at this stage the tragic death of the two young men in Townsville is being treated as deaths in custody (police pursuit)," he said in a statement provided to SBS News.

"This status could change however."

A report is currently being prepared for the coroner and an investigation has been launched into the conduct of police officers in the lead up to the deaths.

It is understood the police had been searching for the men after an alleged attempted looting at a nearby Dan Murphy's liquor store at the height of the floods on Sunday evening into Monday morning (February 3-4).

"The Ethical Standards Command will investigate the matter for the State Coroner with oversight by the Crime and Corruption Commission," Queensland Police said in a statement on Tuesday.

According to The Guardian's Deaths Inside: Indigenous Australian deaths in custody database, more than 400 Indigenous people have died in police custody since the 1991 royal commission into the issue.