At issue is whether such structures are simply designed to minimise tax.
IRD disputes a $12.4 million deduction claimed on the interest of Frucor's notes between 2006 and 2009, plus the use of interest of some $4.9 million. The tax department will impose penalties of $3.7 million if its case succeeds.
Separately, IRD will pursue Frucor for a non-resident withholding tax (NRWT) liability for the March 2008 period of $8.3 million, plus interest of $3.4 million and penalties of $4.2 million.
"In adopting this position, the Commissioner has accepted that the assessments for income tax and NRWT cannot both ultimately be enforced," Frucor said.
"Inland Revenue has advised that if it is decided that the income tax adjustments are not correct, they will seek to impose non-resident withholding tax."
Frucor insists that neither of the tax department's assessments are correct and is continuing with formal dispute procedures, it said.
The company's financial statements show net profit of $32.8 million for calendar 2011, up from $25.4 million a year earlier.
The drinks maker and distributor clamped down on costs, lifting operating profit by 47 per cent to $39 million as revenue rose just 2.6 per cent to $415.5 million.
Frucor paid out $51.2 million in royalties last year, 6.9 per cent less than in 2010. The drinks company holds the bottling licence for Pepsi soft drink brands.
The cost-cutting didn't eat into wages, with personnel expenses rising to $47.7 million from $46.7 million a year earlier.
In January, Japanese parent Suntory Holdings said Frucor revenue was affected by last year's earthquakes in Canterbury and flooding in Australia, though V sales underpinned annual revenue.
"Efforts to further expand sales of V will be mounted in 2012," Suntory said.
"Frucor will undertake to reinforce V's number one category position, particularly by developing the market for a new flavour in New Zealand, and will also endeavour to grow sales of other carbonated beverages."
The Japanese company has said it was aiming for 5 per cent year-on-year sales growth in 2012 for Frucor to 33.6 billion ($528 million).