Wealthy property owners and their estate agents had hoped for a reprieve in this week’s Autumn Statement from higher rates of stamp duty that have slowed purchases of expensive homes by almost a fifth.

Instead, they received a hostile message from the Treasury: a three percentage-point stamp duty surcharge that not only makes buying a second home or investment property more expensive, but may signal yet more measures to dampen the buy-to-let market.

“It’s tightening the noose around property as an investment class,” said Charles McDowell, a London buying agent.

“Every time we say ‘This has got to be it’, and then [the chancellor] has another attack. I’ve had clients on the phone all day asking what to do.”

Analysts agree the new charge is significant not only because of its effects on the economics of owning multiple homes, but as a sign of the changing relationship between the Conservative government and property owners.

“[The government] has talked of its dissatisfaction that the tax system favours investors over owner-occupiers . . . We believe that the government’s preference for home ownership is likely to yield further reforms,” said Jon Bell, an equity analyst at Barclays.

He suggested the chancellor, George Osborne, might opt to ban up-front lettings fees, already forbidden in Scotland, or accelerate measures already announced to withdraw higher rate tax relief on buy-to-let mortgage payments.

The Treasury is expected soon to grant powers of regulation over buy-to-let loans, which make up 16 per cent of mortgage lending, to the Bank of England’s financial policy committee. The move, a response to concerns over financial stability, could result in curbs on loan-to-value ratios.

In another dampener, the Treasury said on Wednesday that from 2019, capital gains tax on sales of residential properties will be due within 30 days, down from 10-22 months.

For at least a million UK residents who own investment properties, it is as if a roof sprang a leak or a tenant stopped paying their rent.

These owners comprise both wealthy investors and middle-class property owners, some of whom use buy-to-let as a substitute for their pension.

“The cosy existence of the property investor, both amateur and sophisticated, has been dealt a sucker punch,” said Russell Quirk, chief executive of the online estate agency eMoov.

The chancellor’s intention is to transform more tenants into owner-occupiers. But while the latest measure will indeed have that effect “at the margins”, said the Institute for Fiscal Studies, it will also have side-effects, including pushing up rents and dampening house price growth.

Stamp duty for the average buy-to-let property valued at £200,000 will more than quadruple from £1,500 to £6,300, according to analysts at Jefferies, an investment bank, while on a £1m home it will rise 66 per cent to £72,600.

Landlords will “churn” their portfolios less often, say the Jefferies analysts, further thinning a housing market that has a lower supply of properties for sale than at any point since the 1970s.

In the already weakening London market, landlords own more than 50 per cent of the housing stock in expensive neighbourhoods such as Mayfair and Marylebone, said Oliver Hooper, director of estate agent Huntly Hooper.

The surcharge could even prompt a fall in house prices and thus hamper development, the IFS warned, while developers said new schemes partly depend on investor-buyers willing to buy before a home is built — a source of upfront finance that could be jeopardised.

Paul Johnson, director of the IFS, condemned the measure as “ill-designed”, a criticism echoed by Adam Challis, head of residential research at JLL, who said measures aiming to boost home ownership did not negate the need for a healthy private rented sector.

“This is yet another targeted intervention into a housing market that is in dire need of long-term decision-making. The raft of policy changes are incredibly disruptive to market activity and create uncertainty that results in dis-investment,” he added.

There are also questionmarks around aspects of the policy, such as how it can be enforced for overseas investors whose principal home is in another country.

Mr Hooper said the latest intervention would likely shift the rental market towards “sophisticated investors using corporate structures”, while the government said it would consult on ways to exempt from the surcharge corporate or fund investors in rental property with 15 or more properties.

This may aid the development of a professionalised “build to rent” sector, with large developments similar to those in Germany or the US.

But for the amateur property investor, the prospects are cloudier than they have been since the financial crisis. Ed Mead, managing director at the estate agency Douglas and Gordon, said: “The government seems to be saying they don’t want people to be landlords.”