The findings of a subsequent investigation by the Australian Transport Safety Bureau highlighting the airline's operating procedures as a key factor leading to the accident were later overturned after they were contradicted by evidence presented at a coronial inquiry into the deaths of those on board the flight.

[1] The safety implications arising from the accident led to a recall by engine manufacturer Textron Lycoming which saw close to 1000 aircraft grounded worldwide while defects were rectified at an estimated cost of $A66 million.

On 21 April 2000, just weeks before the accident the original chief pilot was approved by CASA and reinstated in the position, after his replacement quit amid concerns about the company management and safety culture.

The 150-page document included nine separate safety recommendations, focusing on the apparent relationship between Whyalla Airlines' fuel mixture practices and chemical deposits from accumulating inside pistons and cylinder heads affecting engine reliability.

It suggested the actions of the pilot in continuing to Whyalla while increasing power on the right engine contributed to it also failing as a result of mishandling and overloading due to extra strain.

The findings of the report were disputed by many in the aviation industry, in particular the emphasis on lead oxybromide deposits formed as a result of the engines running at high temperatures due to the company's fuel saving policies.

The conduct of the ATSB during the inquiry was described by the court as "uncooperative and defensive" after reviewing scientific evidence which contradicted the report, indicating that the initial failure occurred in one of the cylinders in the right engine as a result of overheating that may have been exacerbated by the presence of lead oxybromide deposits.

[10] The inquest was critical that the ATSB had not taken into account as many as 15 similar engine failures leading to Textron Lycoming's recall, including two that occurred in Australia after the accident.

Just days before the report was released in December 2001, the Bureau was notified of an incident involving a Sharp Airlines Piper Chieftain which suffered a broken crankshaft in one of its engines.

[12] It argued however that while it was not the ATSB's job to attribute blame in an accident, the Coroner's investigation commissioned experts including representatives from a US firm acting on behalf of victims families in a civil litigation case seeking damages from engine manufacturer Textron Lycoming.

[13] As a result of the investigations into the crash of Whyalla Airlines 904, the Civil Aviation Safety Authority accepted and acted upon some of the recommendations made by both the ATSB and the South Australian Coroner.