The Methodist church, Baptist Union of Great Britain, Salvation Army, Church of Scotland, Scottish Episcopal Church, Quakers in Britain and United Reformed Church all call on the Conservative leader to consider the well-being of the poorest in society and not to ignore evidence that they argue shows the poorest will suffer most from leaving the European Union without a deal.
Currently, the law states that Brexit will happen on 31st October unless the law is changed. Mr Johnson has promised this will happen "do or die".
He has called Theresa May's Withdrawal Agreement "dead" and accepted that no-deal might be the only way to leave in 3 months' time.
The church leaders from across the UK say they have a particular concern about the number of people already homeless, in debt and using food banks.
Their letter reads: "we are compelled to write expressing our urgent concern about your position that leaving the European Union without a deal is acceptable. Advice and data from multiple reputable sources, including the UK Government, indicate that failing to agree a deal will hit those held back by poverty very hard indeed.
"The UK imports 10,000 shipping containers of food from the EU each day. These containers are part of long and complex integrated supply chains. Even minor disruptions to this chain have in the past rapidly had serious consequences. A no-deal Brexit will cause a huge and potentially crippling disruption. Government and many other reputable sources highlight the immediate risk of shortages and price rises. Over the longer term they point to the costs of new and less fluid supply chains increasing food bills for families."
The church leaders, which include the new President of the Methodist Conference, Revd Dr Barbara Glasson, and Rev Lynn Green, General Secretary of the Baptist Union of Great Britain, wrote that the Trussell Trust gave out 1.6 million three-day supplies of food and say: "we believe it is irresponsible to consider a course of action that is expected to make that situation worse."
They also raise concern over energy and medical supplies and point out that many of the difficulties potentially caused by a no-deal exit "can only be tackled in collaboration with the EU" and say that the government are taking a gamble in assuming the EU will co-operate without an agreement, something they call "a huge gamble to take with the basic needs of our poorest citizens and communities."
"The impacts of a no-deal Brexit are at best highly uncertain, and at worst deeply worrying. Our view that it would put at risk the welfare and safety of the poorest communities in the UK is formed on the basis of the best available evidence, including our presence in local communities in every part of the UK. It is notable that assurances about our ability to cope with a no-deal Brexit, while frequent, are yet to be supported by substantial evidence.
"Evidence-free dismissals of well-founded concerns are at this stage both dangerous and inappropriate. Your government's willingness to embrace a no-deal Brexit places upon it a responsibility to demonstrate that the most vulnerable in our communities, those locked in poverty, will not be harmed."
They finish by asking that Mr Johnson's new government to publish urgently its current evidence on the impact of a no-deal Brexit on disadvantaged communities and for him to listen to evidence from communities.
"We assure you of our prayers as you take up this challenging new role."
The full signatories are Revd Nigel Uden, Moderator of the General Assembly of the United Reformed Church; Mr Derek Estill, Moderator of the General Assembly of the United Reformed Church; Professor Clive Marsh, Vice-President of the Methodist Conference; Revd Dr Barbara Glasson, President of the Methodist Conference; Revd Dr Richard Frazer, Convenor of the Church and Society Council of the Church of Scotland; Rev Lynn Green, General Secretary, Baptist Union of Great Britain; Rev Alan Donaldson, General Director, Baptist Union of Scotland; Reverend Judith Morris, General Secretary of the Baptist Union of Wales; Most Revd Mark Strange, Bishop of Moray, Ross and Caithness, Primus of the Scottish Episcopal Church; Commissioner Anthony Cotterill, Territorial Commander, The Salvation Army; Paul Parker, Recording Clerk for Quakers in Britain.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.