An ATO spokesman said 56 public companies with a turnover of between $100 million and $5 billion had received an offer allowing them to determine, at their own cost, situations where it was more "efficient and effective" to have a company auditor review and verify tax information rather than the government agency.

"Our initial assessment is that the pilot results have been encouraging and overall feedback from taxpayers and industry has been positive," the spokesman said.

The so-called external compliance assurance process (ECAP) is designed to reduce costs at a time when the agency is reeling from significant budget cuts under the Abbott government.

It comes as the government turns the heat up on corporate tax avoidance, with a Senate inquiry expected to call on the heads of Australian and foreign multinationals to explain their tax affairs.

Shadow assistant treasurer Andrew Leigh said the pilot program needed to be heavily scrutinised in light of profit shifting by large multinationals.

"If it wants to allow more big companies to audit their own books, the Abbott government should first make available all the evidence from the tax office's pilot program," he said.

The decision to push ahead with the ECAP pilot program, due to be evaluated in March, follows the release of Apple's latest local accounts, which showed the tech giant paid just $80.3 million in Australian tax last year, despite making more than $6 billion in local revenue. It made a pre-tax profit of $252 million.

Multinational companies including Apple have been criticised for booking revenue overseas, in low-taxing places like Ireland or Singapore, to minimise their reportable profit and therefore their taxes in places like Australia.

Under the ECAP plan, lead by former KPMG partner ATO Commissioner Chris Jordan, the big four accounting firms will be able to conduct audits of their clients instead of the tax office.

The plan has been criticised by government officials and union groups, as well as people within the department.

In a recent survey by the Community and Public Sector Union, ATO staff described the plan as akin to "giving the keys to the vault to the thieves".

But the ATO defended the program on Friday, saying it remained "in control of the procedure and outcomes".

It said all auditors were bound by a professional code of ethics overseen by the Auditing and Assurance Standards Board, which would remove the risk of conflicts of interest.

Accounting firm PwC was at the centre of deals to secure favourable tax rates for Australian and foreign multinationals with the Luxembourg government.

The so-called "Lux leaks" was one of the biggest  exposes of confidential tax data, revealed by the International Consortium of Investigative Journalists last year.

Luxembourg authorities are now prosecuting the 27-year-old whistleblower behind the leaks, former PwC employee Antoine Deltour.

An ATO staff member told the CPSU that in light of PwC's role as the architect of the Luxembourg schemes, it seemed "incredulous that the ATO would, a) continue to hire them as consultants and b) continue to consider ECAP an ethically sound proposition".

The Tax Justice Network has written to its members to urge the Luxembourg government to drop its case against Mr Deltour. It is also calling on Foreign Affairs Minister Julie Bishop to intervene.

The Tax Office was one of the agencies hardest hit by the Abbott government's cuts to public service, which saw the agency shed 3000 jobs and make plans to cut a further 1700 by 2018.

It will report on the ECAP pilot program in March, when it is expected to make a decision on whether  to make the program permanent.