The latest Consumer Price Index figures from the Australian Bureau of Statistics shows fruit prices went up 19.5 per cent in the September quarter, while vegetables went up 5.9 per cent.

The increases marked the largest price rises during that period.

"The rise in fruit and vegetable prices is due to adverse weather conditions, including floods, in major growing areas, impacting supply," an ABS statement said.

Ziggys Fresh owner Ken Irvine challenged the figures.

"I'd love to know what's in the basket they're basing that off," he said.

Mr Irvine said while weather events had an impact on prices, customers generally catered their basket to suit.

And prices that rose rarely stayed high for long, he said.

"Nine times out of 10 there's an alternative," Mr Irvine said.

However, Mr Irvine warned that potato lovers might be in trouble, with heavy rains significantly impacting on supply.

Nature's best vegetable is retailing at an average of $5 a kilo, compared to the usual maximum of $2.99.

"With the floods, the two biggest potato growers lost 100 per cent of their crops," Mr Irvine said.

The ABS fruit price figures were based on the price of a fixed basket of goods across a variety of outlets, then analysed by ABS staff, ABS CPI director Andrew Tomadini said.

CPI rose 1.3 per cent through the year to the September quarter.

Electricity rose 5.4 per cent and tobacco increased by 2.3 per cent, while fuel fell by 2.9 per cent and communications by 2.3 per cent.