What do you do when confronted with 1,300 tonnes of stinking, rotting fish in hot, summer conditions in a region traumatised by a significant bushfire?

That was the situation that faced Brad Flaherty after the destructive fire struck South Australia's southern Eyre Peninsula in January 2009.

Until now, the former Port Lincoln police superintendent had not spoken publicly about the details of what was a potential public health emergency.

But he has now outlined to the ABC his actions as zone co-ordinator during the fire's aftermath, with the proviso that some details remain confidential — including the eventual pilchard burial site.

The problem began after the bushfire destroyed two fish factories — one of which contained 1,300 tonnes of imported Californian frozen pilchards used for tuna feed.

The pile was estimated at about the size of six two-storey homes.

"They created a significant health risk and a danger to local fish populations because they were not cleared by [the Australian Quarantine and Inspection Service]," Mr Flaherty said.

The fish were "horribly going off", he said, but could not be buried in the local dump because that was still on fire.

"The then-commander of the MFS gave me a ring and he said 'Brad - we've got a real problem with these pilchards'," Mr Flaherty said.

"I started laughing at him actually. I said 'yeah, well that's your problem mate - you better fix it up - I don't know what you're going to do'.

"He said 'no - it's yours - you're the zone co-ordinator - you have to deal with it'."

Flames rage near houses during the Proper Bay bushfire in 2009. ( Michael Sleep: User submitted )

Quarantine concerns created disposal dilemma

A number of options were considered, including composting the fish or taking them to Whyalla, but both of those were rejected because of quarantine concerns.

"[The pilchards] couldn't be dumped at sea. We were worried about the seabirds taking them off," the former superintendent said.

"We considered burning them in situ but because of the psychological profile of the township having just got over the bushfire we couldn't do that - and it wouldn't have been efficient."

The solution was to find a site to bury them - and quickly - as birds were starting to spread them round the city.

Adding to the emergency was a massive, growing stench and increasing public health concerns, but it was not as simple as digging a huge hole and burying the pilchards.

Brad Flaherty was charged with the task of disposing of the pilchards. ( Supplied )

Myriad issues included ensuring a suitable site so that the region's valuable water table was not compromised.

"When you're dealing with - for example - sheep or cows or something like that that's been impacted by a disease or been impacted by bushfire there's things called staff tables which will give you an indication as to the sort of hole you've got to dig," Mr Flaherty said.

"They've got calculations as to how many carcasses you can put into various size holes.

"For example, you dig a hole the size of an Olympic swimming pool and you might be able to put 300 cows in there.

"Well I can tell you, there was actually no staff table for dead fish - nothing."

But with the combined knowledge of a recovery engineer and fishing industry representative a suitable sized pit was reached - 20 metres by 40 metres by six metres deep.

"If we hadn't have done it we would have been in all sorts of trouble from a health perspective," Mr Flaherty said.

"There were huge costs involved. there were a lot of negotiations that had to go on behind the scenes with a lot of organisations, a lot of personalities.

"We pulled it all together in three days."

Smoke over a field from the Proper Bay bushfire. ( AAP )

Mr Flaherty said his career as a police officer had seen him involved in "some pretty hairy sort of stuff" and said the pilchard operation was "one of the most complex things I've had to do".

But he said there were some critics of the way things were handled.

"That was probably because they didn't have the full facts... and because there were commercial implications I didn't want to push it too far into the media. I'm hoping all the dust has settled," he said.

"But of the flak we got, there was none from the official side... the commercial interests were happy and things are pretty smooth now I think."

So is there somewhere on the outskirts of Port Lincoln that would be an extremely good place to plant tomatoes this summer?

"I would suggest that's a good point," Mr Flaherty said.

"If you wanted them you could grow them pretty well - but I'm not going to say where it is."