The exemption will only apply if the pub is the only pub in the village.
Its comes as the Home Office issued its response to the consultation on the levy and early morning restriction orders (EMROs), which will affect pubs and other licensed premises that trade after midnight.
The late-night levy will charge all premises in a local authority area that are authorised to sell alcohol between midnight and 6am.
In its response to the consultation on the measures - ‘Dealing with the problems of late night drinking’ - the Home Office said:
“The Government is committed to protect local pubs where they are seen to be important community asset."
Whilst relief from the levy is not yet available for Wales, the Home Office is currently working with the Welsh Government to explore a suitable exemption for Wales.
Among other decisions on the two measures, the Home Office said that people affected by an EMRO will have 42 days to make relevant representations for against its introduction.
EMROs will prevent the sale of alcohol between the hours of midnight and 6am in licensed premises within a certain area, whilst the late-night levy will collect a fee from premises which open past midnight. Both measures form part of the Government's Police Reform and Social Responsibility Act.
The Home Office said that licensing authorities will be required to notify licensed premises that would be included in the scope of a proposed EMRO, rather than all licensed premises in the licensing authority area.
It added that EMROs will not apply on New Year’s Eve after 73% of respondents to the consultation agreed with the proposal. The same will apply for the late-night levy, with 66% agreeing it should not apply on New Year’s Eve.
Whilst there will no exemptions from EMROs, premises which offer a mini-bar and room service will be able to continue doing so under the proposals.
Minister for Crime Prevention and Antisocial Behaviour Reduction, Lord Henley said: “The Government is radically reshaping its approach to crime and policing by giving back powers to local communities so they can reclaim their high streets.
“We have already overhauled the ineffective licensing regime and introduced new measures that will put local people back at the heart of licensing decisions, allowing them to take action against problem premises and alcohol-related offending.
“We are building on this through the government’s new alcohol strategy which sets out plans to crack down on the ‘binge drinking’ culture, end the availability of cheap alcohol and irresponsible drinks promotions, and slash the number of people drinking excessively.”
The Home Office intends to commence the provisions containing the framework for EMROs and the late-night levy in October.
Guidance in relation to EMROs will be included in statutory guidance issued under section 182 of the 2003 Licensing Act.
Separate guidance on the levy will be published on the Home Office website.
British Beer and Pub Association (BBPA) chief executive Brigid Simmonds said: “We are pleased that the Government has listened to many of the BBPA’s concerns, but there are real doubts that this legislation is necessary.
“They have listened and backtracked on the wide number of exemptions they were planning, as this would have been grossly unfair on community pubs.
"We also welcome the inclusion of Business Improvement Districts (BIDs) as a discretionary exemption from the Levy, as well as other good practice schemes which are to be recognised for discounts.
“However, a Government that says it wants to cut red tape still has to match words with deeds. There are already enough powers for police and local authorities to tackle late-night problems.
"The Levy still has the potential to be complex, unwieldy and problematic for both businesses and local authorities. At the end of the day it is partnership schemes like BIDs, Best Bar None and Pubwatch which work best.”