A 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 an investigation into the sinking, a court has heard.

As a result, the investigating officer says he can no longer stand by his report.

Blacked out portions of the report into Australia's response to the sinking of the Siev 358, which was kept from a police investigation into the incident.

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

A total of 104 men died in the incident.