A Treasury official has admitted a tax loophole will allow the targets of the Abbott government's deficit tax to avoid paying hundreds of millions of dollars in revenue.

The Abbott government will introduce its temporary ''deficit tax'' on July 1 for high-income individuals with taxable income over $180,000 a year.

The tax, which has Labor's support, is expected to raise $3.1 billion and will run for three years.

The budget forecasts it will raise $600 million in 2014-15, and $1150 million in 2015-16.

But when asked in Senate estimates on Thursday why Treasury believed the tax would raise $550 million more in its second year, the head of Treasury's revenue group, Rob Hefferan, said the ''vast bulk'' of the difference was due to a tax loophole.

As explained, the government's 2 per cent deficit tax will see the top marginal tax rate increase from 47¢ to 49¢, and to prevent taxpayers from using fringe benefits to avoid the tax, the fringe benefits tax (FBT) rate will also be increased to 49 per cent.

However, it will only rise to 49 per cent from April 1, 2015 - nine months after the introduction of the deficit tax. That means the FBT rate will be 2 percentage points lower than the top marginal tax rate for nine months.

When asked how much revenue would be lost with the tax rates, Mr Hefferan said: ''I think we'd be able to say unequivocally that the vast bulk of that [$550 million difference] would be as a result of FBT.''

He said the decision to raise the FBT rate nine months after the deficit tax was due to Treasury's wont to align the FBT increase with the FBT year, which runs from April 1 to the following March 31.

''If the proposal is that the FBT [change] should have occurred on 1 July, 2014 … the compliance costs for employers, in dividing the FBT year like that, we would take that to be pretty onerous,'' Mr Hefferan said.

Shadow assistant treasurer Andrew Leigh said the loophole was a concern as hundreds of millions of dollars would be forgone.

Finance Minister Mathias Cormann said the former Labor government's Queensland flood levy was structured the same way. But Mr Hefferan said the FBT rate was not changed there because the levy only lasted for one year.

''For the flood levy, the idea of people rearranging their [tax] affairs for only one year was considered to be pretty low risk,'' he said.

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