A safety net for monitoring chemicals in Australia's domestic food has been axed by the Federal Government, the ABC has discovered.

Government reports have identified significant gaps and deficiencies in Australia's agricultural chemical residue produce monitoring, as testing varies in each state and territory.

The Labor government established a $25 million, five-year pilot in 2013 for a National Produce Monitoring System, which aimed to give consumers confidence and act as a vital safeguard.

The system was scrapped in the finer detail of last year's budget.

"[It was] $25 million we were prepared to spend on what I think was a program of great merit," Labor's agriculture spokesman Joel Fitzgibbon said.

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"We are living in an environment where there is no bigger issue than food safety and I think the Government has some questions to answer."

A spokesman for Agriculture Minister Barnaby Joyce argued it was not the Federal Government's responsibility and that the axing was a savings measure.

"[The system] was a put forward as a budget savings measure as the Commonwealth has no power to enforce compliance with the domestic use of agricultural chemicals," the spokesman said.

"This responsibility lies with the states and territories."

Every state and territory agreed in-principle that a national monitoring system was necessary in April 2012, signing off on the idea at a Standing Council on Primary Industries meeting.

"An enhanced produce monitoring program coordinated across Australia is required to ensure an increased level of confidence for consumer safety, allay potential trade concerns and to ensure validation of chemical regulation," the Decision Regulatory Impact Statement for the changes said.

"The proposed targeted national approach to produce monitoring, tracebacks and sample analysis would provide additional safeguards in validating the system, allaying trade concerns and mitigating against any risks of illegal chemical use on around annual agricultural production of $50 billion, including $12.53 billion worth of exports of produce from minor crops over 10 years."

The Federal Department of Agriculture declined to reveal to the ABC results it has produced thus far, saying there was only limited sampling and the pilot methodology was unsuitable for publishing.

But in a random test for the system in Western Australia last year, six violations of pesticide limits were reportedly found in 80 samples of apricots and peaches.

"If the data hasn't been released, well that's a great disappointment," Mr Fitzgibbon said.

"It means that the $5 million at least we spent in year has been completely wasted."

99 per cent of produce below safe pesticide levels

The Government conducts some level of testing for chemical residues, known as the National Residues Survey (NRS).

It tests key export produce, some but not all horticulture, grain and meat products.

Its most recent results show more than 99 per cent of tested produce is below safe pesticide levels.

"The Commonwealth's main role in this space is to monitor imported food ... and some exported food [through the NRS]," a spokesman for Mr Joyce said.

"Food Standards Australia New Zealand conducts the Australian Total Diet Study regularly, which assesses consumers' dietary exposure to pesticide residues, contaminants and other substances."

But the NRS only provides an annual snapshot, not ongoing monitoring as Labor's system was designed to do.

Big supermarket chains conduct their own quality assurance, but the results are not made freely available.

Murdoch University grain residue specialist, Associate Professor Rob Trengove, said there was room for openness and improvement in Australia's system, especially compared to Europe.

"They tend to do more testing than we do and they also have the advantage that a lot of it is very much regulated," Associate Professor Trengove said.

"Regulatory authorities require that [data] and that information has to be made available for people to use it.

"So Europe is quite well advanced in terms of determining what the average exposure that people might have to pesticides actually is."

Associate Professor Trengove said he hoped the information collected and available eventually reaches higher standards.

"I think the big thing that we really have to be very cognisant of is that individuals will respond to different levels of chemicals in the environment as well as chemicals in their food," he said.

"To some extent in the long term we need to deal with that on a one-on-one basis.

"What someone can eat and have absolutely no problems may cause some health issues for other people."