A crucial top-secret report into the Australian authorities' response to the distress of the ill-fated asylum seeker boat known as the SIEV 358 was deliberately withheld from a West Australian police investigation into the sinking that killed 104 men.

The West Australian Coroner's Court has been told that a Australian Federal Police agent had told Customs and Border Protection and the Department of Defence not to give the classified document to the police officer who had been asked to investigate the sinking on June 21 last year as a major crime.

Desperation: Occupants of the SIEV 358 on the boat's hull.

The West Australian officer in charge of the investigation, Detective Inspector David Bryson, told the court he had no idea that information had been hidden from him until he arrived at court on Friday morning.

He he had top secret clearances which meant he could have seen any classified or secret information, but he was never told it existed.