He was responding to a confidential leaked draft transport strategy from February, advising that transport pricing needs to reflect the true cost of using the state's roads.
"Charging for road use at certain locations or times can encourage customers who have flexibility to choose other options," the document, reported by Nine, says.
Mr Perrottet dismissed suggestions of such a tax.
"There is no plan for a congestion tax and and we can rule it out completely," he told reporters on Wednesday.
A congestion tax was introduced in London in 2003, with drivers paying about $25 over a 20-square-kilometre radius of the city.
Mr Perrottet said the government encouraged its public servants to come up with new ideas and think broadly and ambitiously.
However, just because the public service advised something did not mean it would be implemented.
"We make the decisions as elected officials, the public service provides advice," Mr Perrottet said.
Congestion taxes had been considered before and ruled out.
Another suggestion was to change public transport fares, which are subsidised, to reflect "the true cost of trips".
The government receives advice yearly from the Independent Pricing and Regulatory Tribunal on public transport fares.
"We weigh that up and we make the decision, but I'm a big believer in subsidised public transport ... it's a great social good," the premier said.
The Labor Party has seized on the report as it prepares to fight next year's election on the cost of living and the impact of transport costs on household budgets.
"Here we go again," Opposition Leader Chris Minns said in a statement.
"The NSW government has run out of money and it's motorists who will pay.
"They say one thing to the camera and hide their plans in secret documents."
Mr Perrottet accused Labor of running scare campaigns on everything the government announces, as well as things it does not.
The leaked report comes amid an ongoing inquiry into road tolls in NSW.
The premier said he wants a fairer system.
"I don't like the fact that every time you move on to a different motorway you're paying a flagfall, that's expensive and that needs to change," he said.
Any change to toll pricing is unlikely to come before the next NSW election in March 2023, as negotiations would need to take place with the toll operator Transurban.
Sydney households spend the most in the country on transport, with an average weekly household spend of $474.44, the Australian Automobile Association reported last week.
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