The new report shows a shortfall of $270 million on a target of $790 million from headline "compliance" efforts, announced by both Labor and Coalition governments since the 2012.

The audit, published on Tuesday found senior bureaucrats at the departments of Human Services and Social Services failed to honour commitments to keep their political bosses and other departments in the picture about how the compliance projects were tracking.

But Human Services, centrelink's parent department, has flatly rejected the criticism, saying it had delivered savings of $998 million from the seven measures against a target of of $788 million, putting it ahead by $210 million

The Audit Office looked at seven of 10 Centrelink-related fraud prevention and compliance announced in budgets from 2012 to 2016 and designed to tackle "existing fraud and compliance risks affecting the integrity of the social security system."

The audit did not examine the "business as usual" anti-fraud effort.

One of the measures was Centrelink's controversial "Employment Income Matching" effort, commonly known as "robo-debt' but the Audit office's findings were limited by the relatively short period of time the program has been underway.

The ANAO's described Human Services' advice to its ministers on the progress of the compliance efforts as "ad hoc" and not consistent with what was promised at the outset.

"Achievements against the expected outcomes from the measures were mixed and the majority of the compliance measures examined did not fully achieve their expected outcomes, including savings and addressing the risks to payment integrity, as agreed," the auditors wrote.

"Where achievements are likely to be significantly lower than commitments, the relevant minister should be promptly advised, to allow for a timely decision on whether the continued implementation of the relevant measure is the most efficient and effective use of public resources in the circumstances."

In an unusually aggressive response to an audit, the Department of Human Services said the Audit office had got its numbers wrong and rejected its key criticisms.

"The department does not accept the key conclusion in the report that most of the compliance measures examined were not effectively implemented and the expected outcomes were not fully achieved, including savings," DHS wrote in its official response.

"In contrast to the report, the evidence demonstrates the department, exceeded expected outcomes from new measures, was effective in the implementation of the Compliance Programme and provided clear and accurate reporting on progress of these measures in both public reporting and briefing to Ministers."

Minister for Human Service Alan Tudge said he welcomed the report and that the ANAO had used different accounting methods to DHS, explaining the difference in figures between the two outfits.

He said the overall anti-welfare fraud effort was going well.

"Across all fraud and compliance activities, the Commonwealth realised $3.9 billion in savings since 2012, with the ten measures delivering savings of $1.44 billion against a target of $1.07 billion, exceeding the target by 35 percent," the minister said.