At present, Union flags are only required to be flown on all UK Government buildings on designated days, but the new guidance from the Department for Digital, Culture, Media and Sport will ask for it to be flown all the time.
Government ministers said the changes would be a “proud reminder of our history and the ties that bind us”.
Housing Communities and Local Government Secretary Robert Jenrick has written to all councils in England in a bid to encourage them to fly the flag on their buildings.
The move will also allow dual flagging – where two flags can be flown on one pole.
Culture Secretary Oliver Dowden said: “The Union flag unites us as a nation and people rightly expect it to be flown above UK Government buildings.
“This guidance will ensure that happens every day, unless another flag is being flown, as a proud reminder of our history and the ties that bind us.”
Mr Jenrick said: “Our nation’s flag is a symbol of liberty, unity and freedom that creates a shared sense of civic pride.
“People rightly expect to see the Union flag flying high on civic and Government buildings up and down the country, as a sign of our local and national identity.
“That’s why I am calling on all local councils to fly the Union flag on their buildings – and today’s guidance will enable them to do that. ”
It comes after the BBC’s Charlie Stayt and Naga Munchetty were criticised for referencing the size of Mr Jenrick’s Union flag during an interview with him last week.
The broadcaster said it had received complaints from people who were “unhappy” about Stayt’s comments and Munchetty’s subsequent behaviour on social media following the incident on BBC Breakfast.
Munchetty has also previously apologised for liking tweets which she said were “offensive in nature about the use of the British flag as a backdrop in a government interview”.
Asked on Wednesday if the Union flag should be more prominent around Wales, Welsh Secretary Simon Hart said: “I think the Union flag is an iconic brand.
“I don’t think we should ever use it for political purposes, though.
“I think that would be a strange thing to do, sort of try and make a political point out of it.
“It is the flag in the UK.
“I think it’s recognised across the world as such and respected across the world as such, just as the Welsh flag is probably as prominent and as as relevant brand in itself.
“I’ve never thought of flags being part of political weaponry, I don’t think they should be.
“My view about the union is it isn’t a political party, and we shouldn’t politicise the union.”