The Australian Tax Office (ATO) has denied reports of a toxic workplace culture where staff are pressured to meet revenue-raising targets and aggressively pursue small businesses.

Former ATO staff have told a joint Four Corners and Fairfax Media investigation they were pressured to hit revenue targets and to take action against individuals who were still appealing alleged debts.

The alleged tactics included an "hour of power" in which tax collectors were instructed to seize funds from the bank accounts of taxpayers assessed to owe the tax office money, regardless of their personal circumstances.

In a statement, an ATO spokesman said the cases highlighted do not suggest "systemic issues" within the organisation.

"The work we have done over the last five years reinventing the client experience and our culture means many of the allegations from these cases are not representative of today's practices," the statement said.

"Where we have made mistakes, we will apologise and seek to rectify the position and restore the relationship with the taxpayer."

Earlier today, Opposition Leader Bill Shorten said Labor would investigate issues raised by the whistleblowers and whether small businesses were being treated fairly.

"The whistleblowers have drawn the nation's attention to something that a lot of businesses and people have been concerned about," Mr Shorten said.

"It looks like people's genuine concerns have some basis in fact."

Mr Shorten said Labor would investigate the allegations when Federal Parliament returns in May.

Sorry, this video has expired Labor to investigate ATO reports

ATO 'can act like judge, jury, executioner'

The joint investigation has prompted tax lawyers, watchdogs, academics and peak bodies to warn the ATO needs new checks and balances to ensure its powers are not abused.

Timeline: Concerns about ATO 2000: Senate committee raises concerns about a lack of oversight, warning there is no way to know whether ATO systems are fair.

Senate committee raises concerns about a lack of oversight, warning there is no way to know whether ATO systems are fair. 2010: The Ken Henry Review recommends a new board to advise the Commissioner on ATO management.

The Ken Henry Review recommends a new board to advise the Commissioner on ATO management. 2011: Bill Shorten, then assistant treasurer, revives the Ken Henry recommendation, saying it will provide advice on ATO culture.

Bill Shorten, then assistant treasurer, revives the Ken Henry recommendation, saying it will provide advice on ATO culture. 2013: Joe Hockey, then shadow treasurer, floats the idea of splitting the ATO: separating police and administrative powers.

Joe Hockey, then shadow treasurer, floats the idea of splitting the ATO: separating police and administrative powers. 2015: Parliamentary committee raises concerns about the ATO's strong powers. Recommends a second commissioner to deal with appeals and reversing onus of proof.

Parliamentary committee raises concerns about the ATO's strong powers. Recommends a second commissioner to deal with appeals and reversing onus of proof. 2015: The Inspector General of Taxation says ATO are more concentrated than other tax agencies. Says policing and administrative roles should be split if concerns continue.

The Inspector General of Taxation says ATO are more concentrated than other tax agencies. Says policing and administrative roles should be split if concerns continue. 2016: Parliament launches new review into ATO external scrutiny. Recommends current levels remain with some tweaks.

Parliament launches new review into ATO external scrutiny. Recommends current levels remain with some tweaks. 2016: Law Council calls for Inspector-General of Taxation to be given greater resources to monitor the work of the ATO.

"The problem here is that you've got tremendous power invested in an organisation which can effectively act like a judge, jury and executors rolled up into one," tax lawyer Graeme Halperin told Four Corners.

Former chairman of the Australian Competition and Consumer Commission, Allan Fels, said the Government should consider splitting the ATO's administrative and policing functions to create an extra level of scrutiny within the organisation.

"The problem stems from the very great power of the Tax Office to make big decisions affecting people's income and lives," Mr Fels told the ABC.

"Normally when such powers are given to someone, we have certain checks on the exercise of that power but for various reasons various governments have let that power go unchecked [at the tax office]".

The idea of splitting the tax office was floated in early 2013 by then shadow treasurer Joe Hockey, who was concerned about the ATO's aggressive interpretation of tax law.

But Mr Hockey didn't introduce the reform when the Coalition came to power later that year.

The ATO was opposed to the reform — warning it would slow down appeals and be ineffective — and the Government instead announced a parliamentary inquiry into tax disputes.

That stopped short of calling for the ATO to be formally split in two, but called a new second ATO commissioner to handle appeals and ensure businesses were being treated fairly.

It also called for the burden of proof to be reversed so that the ATO needed a higher standard of proof before launching debt collection action.

Those recommendations were rejected by the Government, although some changes have been made within the Tax Office.

Peak body calls for change

When Mr Hockey floated the idea, industry groups like the Institute of Chartered Accountants adopted a watch-and-see approach, saying commissioner Chris Jordan had only just been installed and he should be given time to make changes.

But now, five years later, it is calling for change, with one senior official at the rebranded peak body describing the Four Corners report as "harrowing".

"Many chartered accountants would agree with sentiments expressed on the Four Corners program about the ATO's powers, particularly their impact on individuals and small business operators," said head of tax at Chartered Accountants Australia and New Zealand Michael Croker.

"Where a taxpayer is trying to do the right thing in a complex, self-assessment tax system, heavy-handed approaches can jeopardise what should be a good working relationship with the ATO."

Mr Croker has also supported inspector-general of taxation Ali Naroozi's call for small businesses to be given stronger appeal rights.

If you run a large business — with an annual turnover of more than $250 million — you can request a review by someone within the ATO who wasn't involved in the initial audit.

But if you run a small business, you can only access in-house mediation.

"The small business group within the ATO should include some wise heads, or some former practitioners, that can look at some of these emerging issues and assure the commissioner they're being dealt with appropriately, and consistently," Mr Crocker said.

Liberal Democrat Senator David Leyonhjelm said he would support reversing the onus of proof and ensuring more oversight of ATO decisions.

"Almost every government agency has to prove its case first, that's the normal way the law works," Senator Leyonhjelm told the ABC.

ATO: We welcome constructive criticism

The ATO has moved to assure taxpayers and small businesses it is listening to industry concerns.

"While we do sometimes make mistakes, we acknowledge those specific instances and we always welcome external feedback and constructive critique," ATO deputy commissioner Deborah Jenkins said.

"We all need to make sure that we are working towards the best interests of those incredibly hardworking and innovative 4 million small businesses around Australia."

Ms Jenkins said she was concerned some business might feel discouraged from seeking help from the ATO after watching the program.

"That's the worst outcome for everyone," she said.