Documents released by the Pike River families show the handling of exhibits from the mine was mismanaged, with the inquiry head at the time describing the chain of evidence as "diabolical".
The revelation casts doubt on whether a potentially crucial piece of evidence to the cause of the explosion, a switchboard door, will ever be found.
The documents are in the form of a debrief conducted by the police in April 2012, looking at what worked and what didn't in the police investigation into the explosion.
It was written by the inquiry head at the time, Detective Superintendent Peter Read, who continues to be involved in the investigation to this day.
It referred to the police body recovery operation and the investigation into what caused the explosion and said the recovery was "disorganised" when it came to keeping proper records, despite being told early on to take notes.
Mr Read said exhibits, including photos and video, arrived at the investigation base with no documentation so they had no idea when or where they had been taken.
He talked about the chain of custody for evidence, where every movement of exhibits was documented to prevent claims of evidence tampering.
In this case the chain of evidence, which Mr Read said was "basic police work", was described as "diabolical".
There were no job sheets or reports for any of the exhibits and at one stage they were given 600 photos of exhibits but had no idea who had taken them or what they were even of.
Cameras bought to help document the recovery operation and the investigation simply disappeared.
While the police were on the look out for any criminal behaviour, the Department of Labour, now known as WorkSafe, were investigating any workplace safety breaches.
Police would often defer to these inspectors who were supposed to know more about mining than them.
However Read talked about them as being "out of their depth".
He noted they were investigating themselves over their own role in the disaster, and asked whether the police should have gone to somebody more independent for advice, such as state-owned coal company Solid Energy.
Fault is found with the Department of Labour's own record keeping, with Mr Read saying much of their findings were confined to note books and they did not have systems in place to manage their own investigation file in a "logical sequence".
He said because of this the police were still missing information.
Mr Read said the Department of Labour interviewed a fraction of the people the police talked to and gathered information that would prove their case, instead of trying to corroborate what people were saying by checking with others, as the police would do.
He notes police will probably not be in a position to decide whether a criminal prosecution is possible until they are able to get into the mine and says they will probably "sit on the fence" until this happens.
On the workplace safety charges, he says these could also be difficult to prove in court given the state of the Department of Labour's exhibits.
In a statement, WorkSafe said it did not exist at the time and had no involvement in the investigation, so it would be inappropriate for it to comment.
Police also declined to comment apart from a short statement which said the debrief was done so they could look for any areas of improvement that could be made. They said the systems in place for receiving exhibits "was highlighted as an area that could be improved".
They said they were in the process of investigating what happened to the switchboard door which would involve talking to those involved in the original investigation.
The statement said Pike River was one of the most complex investigations ever carried out by police.
Read the debrief: