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Serious shortfalls in Australia’s monitoring of pesticide residues in food, particularly food destined for the domestic market, were identified by the federal agriculture department nearly a decade ago, documents obtained by Guardian Australia reveal.

Bureaucrats in the department expressed concern about Australia’s food monitoring as early as 2014, the documents, obtained under freedom of information laws, show.

A $25m five-year pilot program for a national produce monitoring system was set up in 2013, but scrapped when the Coalition came to power and Barnaby Joyce became minister. The results have never been released.

Testing of food sold in Australia is largely left to the fresh food markets under a self-regulatory system. In general, growers are required to submit samples once a year. There is no routine screening by state or federal health authorities or by Food Standards Australia New Zealand.

Some food for export, notably meat, is tested as part of the National Residue Survey (NRS), but the documents obtained by Guardian Australia reveal the department has identified shortcomings in this system as well.

Earlier this year the department engaged a consultant to establish where it lacked data.

“The department has little information about the presence of agvet [agriculture and veterinary] chemicals in treated produce sold domestically within Australia,” one document from April 2022 says.

“There is little data currently available to the department regarding human health or environmental fate of agvet chemicals in Australia in ‘field’ conditions,” it says.

“The paucity of available ‘field’ data poses risks to the Australian government in both policy development and in international fora, when discussing the integrity and effectiveness of the Australian regulatory system.”

A spokesperson for the department said: “The tender should not be taken to mean that there is no monitoring, or that monitoring is lacking. However, monitoring is often undertaken by these groups independently of one another, without national collaboration or consistent reporting practices.”

The documents also spell out how the government has no real idea about the impact of agvet chemicals on the environment and that work is needed not just to pull together data from the state environment authorities, but also independently run soil and water testing.

The final report of the independent review of the pesticides and veterinary medicines regulatory system in Australia two years ago recommended the establishment of an environment monitoring program to detect levels of pesticides, parasiticides and antimicrobial drugs in the environment.

The spokesperson said the government was considering recommendations related to residues testing made in the review.

Other documents reveal further concerns about the NRS, which covers only a limited number of products for export – mainly meat products.

In the documents, from February this year, the department acknowledges it is not in a position to verify the results of the survey that appear on its website because the actual testing is done by industry bodies using private laboratories.

In 2014, Greg Read, then the first assistant secretary in the agriculture department, responded to a proposal to introduce more comprehensive residue testing for fish products for export.

“Agreed. Difficult to certify without a credible residue survey program. Keep at it,” he wrote.

But after 2014, monitoring was wound back with the abandonment of the pilot broader survey.

In March this year matters came to a head, amid queries from the European Commission about Australia’s system and a requirement to lodge details of Australia’s monitoring system.

“Currently there is no formal requirement for participation in a recognised monitoring program in the export control rules (other than for poultry through AS4465),” Anna Somerville, the head of export controls, wrote in February.

“The department currently relies on the cooperation of industry. Comparable countries such as New Zealand, Canada, United States and member states of the European Union have national residue monitoring programs in place across multiple commodities.”

The Cattle Council of Australia also raised concerns about the reputational risk to Australia’s beef trade, noting incidences of “non-tariff measures” being applied to Australian meat exports at ports around the world because of detections of residues.

In October 2021 Australian Country Choice in Brisbane had its trade to China suspended after customs officials at the port of Ningbo allegedly found residue from the banned chemical chloramphenicol on beef products. It was one of 10 meat exporters to have its licence suspended by China.

The cattle council said “a national whole-of-industry integrity system that delivers consistency in policy across the whole supply chain and guarantees food safety and global consumer confidence in Australian beef was a priority”.

It wanted the agriculture department to stump up nearly $800,000 to design a new system.

The documents also reveal that the traceback system – which is used to find the origin of the contamination in exported meat – has problems.

“Existing contractual arrangements between NRS and jurisdictions require completion of traceback investigations within 28 days of when the traceback is initiated,” one document says.

However, a review of 285 residue violations since 2014 selected at random found that only 34% of all traceback investigations were completed within a 28-day timeframe, with an average total time elapsed of 100 days and a median of 42 days.

“The time taken to complete these investigations is untenable and requires correction,” the department said.

Asked about the delays, the department said tracebacks were the responsibility of state and territory governments.

In February, the department called for expressions of interest from veterinary facilities to provide an assurance system for the NRS because it was not able to provide verification to trading partners about the certificates being provided by Australian producers.

The tenderer would be required to dose animals with known quantities of specified agricultural and veterinary chemicals that can potentially cause problems in meat and then harvest tissue samples from the animals to determine residues.

The results would be used to verify the performance of the laboratories being used by meat producers.

“As with all countries, Australia occasionally detects residues that require attention,” the department said.

“Additionally, importing countries occasionally detect residues in Australian exports that require investigation. Investigations of these detections has not indicated levels of concern for consumer health and importantly determined the residues were not due to illegal use.”

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