Deputy Prime Minister Paula Bennett says the Government's been sending mixed messages on water because the issue "just hasn't been on the radar".
On Tuesday it was revealed a water company based in China, Nongfu Spring, is trying to get consent to remove 5 million litres of water a day, virtually for free.
Environment Minister Nick Smith earlier this week said charging companies to remove water was ridiculous.
"If parties opposite want to start imposing new taxes on the use of water, where are they going to stop? Will air be charged for next?"
On Thursday however, Prime Minister Bill English said the Government had to "work through all the existing issues around water about how the history of first-in, first-served started and what the transition might be".
Ms Bennett said on Friday morning the confusion is because they've "never" thought about charging for it.
"It just hasn't been on the radar. We never have. It's come up more recently," she explained on The AM Show.
"I don't think it's the biggest issue around water right now. I'd have to see all the ins and outs."
Labour deputy leader Jacinda Ardern said putting a price on the country's water is a "bottom line".
"Kiwis have already spoken to this," she told The AM Show. "The idea that you've got a public resource being used for private profit, we usually apply royalties to things like minerals, oil, gas, even gravel. Why wouldn't we do it for water?"
Ms Ardern said the Government's muddled response to the growing backlash shows how out of touch it is when it comes to water issues.
"You can come out of a river with slime all over you and that's considered swimmable - people are really irate about that, and for good reason."
New Zealand First leader Winston Peters has also called for a royalty on water.
Oil royalties earned the Government $193 million in the year to June 2016, down more than 25 percent on the year before.
The Government takes either 5 percent of a company's net revenues, or 20 percent of the accounting profit, depending on which is greater.