The original draft of Finance (No2) Bill indicated that annexes would be caught by the new rules, although the properties are generally not sold as a separate transaction to the main property sale.

The issue was raised in parliament by Sir Eric Pickles, Conservative MP for Brentwood and Ongar, earlier this week.

Speaking in the House of Commons on 11 April, David Gauke, financial secretary to the Treasury, told MPs: ‘I have been made aware that the Bill as drafted might lead to some main houses with an annexe for older relatives attracting the higher rates of SDLT intended to apply to additional properties.

‘I am happy to ​reassure the House that that is not our intention and the government will table an amendment in Committee to correct the error and ensure fair treatment for annexes.’

The treatment of annexes is not a new issue but had to be reviewed in light of changes to council tax which, equally, wanted to treat annexes as a defined separate entity for council tax purposes. This issue was championed by Pickles and eventually councils backed down on their initial proposals.

Gauke added: ‘We certainly do not want to discourage people who wish to create an annexe for an elderly or disabled relative, providing them with support close at hand.’

The amendment to the higher rate levy will be issued at Committee stage and will clarify that annexes will not be subject to the 3% SDLT surcharge.

A Treasury spokesperson told Accountancy: ‘There is an important distinction to understand – an annexe that is part of the home is not sold as a separate home, the question is whether it is capable of being sold as a separate sale.

‘The change that we announced is that if it is sold, it will just be seen as part of the main residence, as a single transaction.

‘It was never our intention for the legislation to work like this and for annexes to capture the higher rate SDLT charge.’

There are a number of criteria under which an annexe qualifies as a single sale transaction – the annexe must be in the same grounds as the main property, will have all the facilities of a main home, and is not worth more than one third of the total cost of the transaction value.

Once the amendment is published, HMRC will publish detailed guidance in advance of the enactment of the new Finance Bill in July 2016.

The higher rate SDLT surcharge came into force on 1 April. It appears that any subsequent sales involving an annex will not be subject to the 3% levy, although it is possible that sellers would have to claim a refund from HMRC in the event of the charge being made. This will be clarified once the HMRC guidance is issued.

Treasury figures indicate that less than 0.1% of annual property sales include an annexe, equivalent to around 1,000 transactions a year.