Prince Charles's plans to build the eco-home of the future and influence government housing policy have run into controversy over the building's ability to satisfy tough new green regulations.

The prince's officials have confirmed that he wants to construct a prototype eco-home from natural materials such as stone and timber, eschewing man-made plastics and insulating membranes.

But because the home will not contain such synthetic materials, critics believe it will not be airtight enough to classify as a zero-carbon house. The government has decreed that all homes built after 2016 should be zero-carbon.

It marks a fresh controversy for the prince just days after an outspoken attack on plans for skyscrapers in London, which he said he feared would become a "rash of carbuncles" on the capital's skyline.

The eco-home will be built at the Building Research Establishment in Watford and will stand next to advanced modernist eco-homes such as Sheppard Robson's Lighthouse and PRP's Sigma Home.

However, while other eco-homes aim to meet level 6 (zero carbon) of the government's code for sustainable homes, Prince Charles's eco-home will be rated at level 3 or 4, according to BRE's director of enterprise and innovation, Jaya Skandamoorthy.

Will Hurst of Building Design magazine, which revealed the prince's plans, said: "Prince Charles will be aware of the problems that the most cutting-edge modern homes have had in reaching the highest levels of the code and is grabbing the opportunity to influence the government's housing plans.

"But whether this pilot house can measure up is doubtful."

The prince's Poundbury village in Dorset has drawn admiration from some traditionalists but opprobrium from many architects.