Senator Dastyari, who chairs the Senate Economics References Committee, has complained Treasurer Joe Hockey approved the decision not to reveal the companies, which are sending billions of dollars offshore as part of apparent tax-dodging strategies.

Tax Commissioner Chris Jordan said in a letter to the committee into corporate tax avoidance that Mr Hockey endorsed his decision not to release the names of 10 resources companies that transferred a combined $31.4 billion to Singapore in 2011-2012.

Mr Hockey said the decision to disclose the information of taxpayers was entirely a matter for the Commissioner of Taxation as an independent statutory office holder.

He said that confidentiality had been a key feature of Australia's taxation system since the 1950s and that "without the continued application of confidentiality provisions, we run the risk of reducing compliance with the system".

He said the Australian Taxation Office's recent amnesty, which saw 5600 people came forward to self-disclose about $600 million in income and $4 billion in offshore assets was an example of how keeping information confidential was beneficial.

"The importance of confidentiality in our tax system has always been respected by both sides of politics," Mr Hockey said, adding that both Opposition Leader Bill Shorten and former Labor treasurer Wayne Swan had cited the importance of confidentiality in previous public statements.

But Senator Dastyari is pushing to have the information of companies suspected of tax avoidance to be made public. He wrote to Mr Jordan on Tuesday asking the ATO reveal the names of the companies channelling money to Singapore, which were redacted by the agency in a document released under Freedom of Information.

Mr Jordan has claimed "public interest immunity" in refusing his request, saying naming companies could undermine confidence in the tax system.

At Wednesday's corporate tax avoidance inquiry hearing in Sydney, Mr Jordan said it would be "unprecedented for taxpayer specific information to be provided in a public way. "As far as I recall, this has not happened before," Mr Jordan said.

The Tax Office needed to maintain "transparent and open relationships" with companies, he said.

"We cannot have a situation where companies cannot share information [with the ATO]," Mr Jordan said, adding that companies might "close down" if their confidential information was revealed publicly.

"It's my judgment that it's better overall for the system to maintain the confidentiality of taxpayer information," he said. "The UK also don't disclose specific information about taxpayers."

Mr Jordan said the Tax Office was already questioning complex tax structures that companies use, including the use of "hubs" in nations such as Singapore.

Singapore is being used by a string of companies, including mining giants BHP Billiton and Rio Tinto, as "hubs" where they shift profits and pay lower tax rates. In 2012-13 alone, Australian companies sent more than $100 billion to related parties to Singapore and another $15.6 billion to hubs in Switzerland.

The use of hubs is not illegal, but has come under question by revenue authorities around the world as they aim to claw back revenue from multinationals.

For years multinationals had "played off" revenue authorities against each other, but Mr Jordan said this would be harder now with new OECD country-by-country reporting requirements being introduced internationally and greater information sharing.

The OECD's head of tax Pascal-Saint Amans has also rejected calls to publicly release country-by-country breakdowns of taxes paid by multinationals, despite growing pressure from community and transparency groups.

But Senator Dastyari said it was a legal requirement for companies to give the ATO this information, and in the public interest.

He said he would write to Ms Laing asking her advice on whether he and the Senate can appeal against the ATO's public interest immunity claim.

Greens leader Christine Milne, who initiated the inquiry, asked Mr Jordan at the hearing whether there was scope for Parliament to changes laws that would force companies in their annual reports to state where their subsidiaries are located, and what the subsidiary's relationship with the parent companies is.

"That's a matter for government," Mr Jordan said.

Mr Jordan has already pledged the ATO will beat a budget target of hitting $1.1 billion in revenue from multinationals by 2017, and expects to clock much of it by the end of the year through audits of technology companies.