Christine Clements told a packed court at the Townsville Law Complex that the coroner's report into the death of the Palm Island man failed to meet deaths-in-custody guidelines.
Mulrunji, 36, was found dead on the cement floor of his cell about 11am on November 19, 2004.
He has been arrested for being drunk and disorderly by the policeman who is the focus of the coronial investigation, Senior Sergeant Chris Hurley.
Ms Clements said the coroner's report made no mention of assault allegations against police.
She said this omission was a "serious error of judgment".
The release of the initial coroner's report, a few days after Mulrunji's death, sparked a riot on the island near Townsville, resulting in the police station being burnt to the ground.
Ms Clements is continuing to deliver her findings from the inquest.
A post-mortem examination revealed Mulrunji suffered four broken ribs, a ruptured spleen, and that his liver was almost split in half.
Police witnesses told the inquest the injuries occurred on the morning of the arrest when Sgt Hurley fell on top of Mulrunji as the two men scuffled and then fell on the steps leading into the police station.
Some witnesses to the incident, islander residents, claimed they saw Sgt Hurley "roughing up" Mulrunji.
The new inquest has lasted 22 months, with sittings at Townsville and Palm Island.
Community leaders have enlisted the help of Brisbane-based lawyer Andrew Boe to convey the findings of the inquest to island residents, in the hope of avoiding a repeat of the 2004 riots.
Mr Boe will use the National Indigenous Radio Service this afternoon to convey the findings to residents, using common language rather than legal terminology.