Fuel prices had already become a highly political topic, but government officials have described recent changes in behaviour as "highly unusual", raising questions about the competitiveness of the market.

Government officials are raising fresh concerns about the competitiveness of the fuel market, saying industry claims would amount to "highly unusual" behaviour.

After Energy Minister Judith Collins put the fuel industry on notice that it was under close scrutiny on Thursday, petrol companies claimed margins had not changed in the way that official figures suggested.

Figures from the Ministry of Business, Innovation and Employment (MBIE) suggest that the margin fuel companies earn on petrol and diesel collapsed to the lowest level in two years in June, but have since bounced back to recent levels.

Ministry of Business, Innovation and Employment Figures calculated by the Ministry of Business, Innovation and Employment (MBIE) suggest petrol and diesel plunged in July, around the time a study into the fuel market was conducted, but have risen strongly since.

If correct, the timing would be suspicious, as the drop occurred just before the release of a government-ordered inquiry into petrol and diesel prices.

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The report concluded that New Zealand's fuel prices may not be reasonable, and that prices had risen far more in Wellington and the South Island than other parts of New Zealand in recent years.

After Collins accused the industry of "cynical" behaviour, Z Energy - which also supplies the Caltex network - hit back at the MBIE figures, which are provisional.

Z Energy spokesman Jonathan Hill said if margins had dropped in the way MBIE had suggested, the company would have had to consider issuing a warning to its investors because of the impact on earnings.

Hill said that in late May crude oil prices and the pump price in New Zealand dropped sharply, and "[a]t the same time the level of price board discounting in the market reduced significantly."

While MBIE said the industry had made claims that margins had been flat during the period, it could raise questions about industry behaviour.

In a statement, a spokesman for MBIE said the industry claims suggested fuel suppliers had changed the "main port" price - the price charged in areas where there is no regional discounting - to be closer to average price across the country, "and then subsequently increased their main port price".

"We are not in a position to understand why fuel suppliers may have done this but stress that it is highly unusual," the MBIE spokesman said.

"It raises questions around the timing of these price changes and the overall competitiveness of the market."

Collins had already dismissed the claims of the fuel companies, saying MBIE's provisional estimates usually tended to be close to the finalised figures, and there was no reason why the figures would be incorrect.

"I take what they're saying with a grain of salt, based on the fact that MBIE has no reason whatsoever to provide incorrect advice," Collins said on Thursday.