Help to Buy has been credited with encouraging Scottish house prices to rise an average of a 3.6% over the last year.
But the Organisation for Economic Co-operation and Development (OECD) said the hikes could prove risky to the economy.
The warning came as the OECD also revised up its forecast for the UK's economic growth. But OECD secretary-general Angel Gurria added: "We are still not out of the woods yet."
Chancellor George Osborne rejected the warning over house prices.
Speaking in Brussels, he said: "I've said we should be vigilant about the housing market and this Government has given the Bank of England the powers, the tools to do that in an independent way.
"That didn't exist before but we've learnt from the mistakes of the last Government and the Bank of England has the tools and independence to do what it feels it needs to do to help to contribute to building that resilient economy."