Michael Matheson has defended the £3 billion upgrade of the A9 after a Scottish Government-commissioned report said a fundamental rethink of large projects was needed to tackle climate change.

The SNP Infrastructure Secretary said dualling the road between Perth and Inverness would remain critical to the Highlands economy in future.

The Scottish Greens accused the Government of rhetoric over substance when it came to the climate emergency.

It followed the publication of the initial report from the Infrastructure Commission for Scotland, which is advising ministers on a 30-year strategy. It covers “both economic and social infrastructure”, including transport, energy, telecoms, water, waste, flood defences, housing, education, health, justice and culture.

It said the Scottish Government’s commitment to offset all carbon emissions by 2045 would have a “significant bearing” on infrastructure. “Compared with past investment... the nature, purpose and focus of infrastructure investment over the 30-year horizon is likely to change fundamentally as we aim for an inclusive net-zero carbon economy,” it said.

Warning of “difficult choices and trade-offs”, it recommended that ministers should prioritise all future infrastructure projects according to how they helped deliver net-zero carbon.

It also stressed the need to make the most of existing assets by enhancing and “re-purposing” them, with a presumption against building new ones.

To help the move to a net-zero carbon economy road network, it said the UK and Scottish Governments should cooperate on a new charging regime as an alternative to fuel duty and road tax.

Last week, it emerged the £1.35bn Queensferry Crossing over the Firth of Forth was already struggling with more vehicle traffic than forecast, barely two years after it opened.

However, Mr Matheson insisted the massive A9 project – seen by environmentalists as a spur to ever more car use – was not incompatible with meeting climate change targets.

He told BBC Radio Scotland: “Even in looking to reduce our carbon output we will always have to have – in moving to a zero carbon economy – we’ll always have to have good road infrastructure.

“The A9 is the largest infrastructure project ever in Scotland at some £3bn. It’s critical to supporting the Highlands economy and the economies of Perthshire dependent on the A9.”

Green MSP Patrick Harvie said: “The Commission seems to be willing to challenge the big differences between the Scottish Government’s rhetoric and action on the climate emergency.

“These include low carbon heating for our homes and buildings, and transport where emissions are rising and the active travel target has been missed by a mile.

“There is no time for the Scottish Government to dither on this, as the decisions made in the next 12 months will shape Scotland’s direction for the next decade.

“That is why the Scottish budget this year should be a climate emergency budget, prioritising low-carbon infrastructure, not a weak placeholder voted through by the Tories.”

Robin Parker of WWF Scotland said: “This is a landmark report and must lead to a revolution in the big projects the Scottish Government spends money on.

“The Infrastructure Committee is right to say that driving a just transition to an inclusive climate-neutral economy must be at the core of investment decisions.

“We’re in a climate emergency and by accelerating our response we can create a cleaner, greener and more prosperous Scotland for all.

“Next month’s Scottish Budget must be ‘climate emergency proof’, shifting investment away from new roads to putting more money into cutting our reliance on the polluting fossil fuels we use to heat our homes and travel.”

STUC deputy general secretary Dave Moxham said the report had “set the right ambitions on inclusive growth and net-zero carbon” and did “not shy away from the enormous challenges presented in areas such as transport and the decarbonisation of the heating system”.

He warned: “The transformation required will not be delivered by the market or by private sector companies operating short-term, profit-maximising shareholdings satisfying business models.

“We need a publicly owned infrastructure company that will provide strategic leadership and set the standards – including employment standards – that we need to ensure inclusive growth is achieved.”