WHK tax principal Scott Mason said if livestock values went up or down, two different tax regimes had "very different" impacts on the amount of tax paid.
"Farmers do have the option of electing to changing the regime to protect the gains if values are going up."
If values went down, farmers could change the regime to deduct the losses, he said.
The structures had been around for a long time but had been highlighted this week by Labour Party claims that farmers were not paying their fair share of tax.
Mr Mason said the wool and meat sectors had been subjected to significant swings in livestock values, from very high to very low in a short timeframe.
This week, a client told him that heifers bought for $1600 a few months ago were now on the market at $1200, a 25% reduction in value in one season.
"You can see how the values fluctuate. If you pick it right, you do well. But if you get it wrong, a deductible loss can become a capital loss."
Revenue Minister Peter Dunne released a statement as part of the Budget in which he said the Government had begun investigating options for fairer rules covering livestock valuation elections.
Under the current rules, farmers usually valued their livestock for tax purposes under one of two valuation methods - the herd scheme or the national standard cost scheme. Substantial differences in values between them were possible.
Under current rules, switching back and forth between the two methods could mean increases in market valuations went untaxed, while decreases in valuation could be eligible for tax deductions, he said.
Mr Dunne also has mixed-used assets in his sights where those assets are used for both private and business purposes.
These would include high-value assets such as yachts and holiday homes which are both rented out and used privately and have provided owners with inflated tax deductions.
Everyone would like to own a holiday home, but it should not be subsidised by the taxpayer, Mr Dunne said.
Both the livestock tax and the mixed-use asset rules were complex. Public consultation documents would be released later in the year, Mr Mason said.
It could be that after consultation, not much was changed, he said.
Mr Dunne also announced that two further aspects of the tax and social assistance treatment of non-cash benefits were to be examined for fairness.
The issues to be considered were whether the definition of income for Working for Families tax credit purposes should be further widened to include more fringe benefits provided to employees and whether salary traded off for non-taxed non-cash benefits should be subject to tax.
