Cabinet secretary Simon Case has insisted the Prime Minister had put keeping the Union together at the forefront of policy making in Whitehall.
Appearing before a House of Lords committee, Mr Case claimed Mr Johnson was “first and foremost responsible for thinking through Union matters”.
He said: “If you’d asked me only a few years ago did I think that devolution or the Union was at the forefront of policy making in Whitehall, I would have said probably not.
“But actually, I think the experience of both Brexit and obviously more recently Covid means that so much more of government, so much more of policy, involves consideration of devolution or union questions much earlier in the process.
“In everything that we do we should be thinking about how it impacts on the Union.”
Mr Case also claimed a culture of “devolve and forget” and the civil service machine had both been radically changed due to the pandemic, to see the devolved administrations work closer together.
The Lords constitution committee also heard Mr Case claim he had rejected the idea of a separate Scottish civil service.
He said: “This government’s position is very clear. We are best operating as one UK civil service across Westminster, UK Government, as well as Scotland and Wales.
“In talking to colleagues currently working in Scotland and Wales and elsewhere, there’s certainly no clamour from civil servants for this. They think they benefit from being part of the wider UK civil service.”
Mr Johnson last week wrote to First Minister Nicola Sturgeon and invited her to a summit to save the Union.
The Prime Minister also wrote to the Scottish First Minister, as well as Mark Drakeford, the Welsh First Minister, saying they needed to show "spirit of unity and co-operation".
Mr Johnson promised to create the title of “minister for the Union” while running for Tory leader, and then gave himself the role after seeing off past leadership contender Jeremy Hunt.
Last year polling showed one of the most persuasive arguments for voters backing independence was the leadership of the Prime Minister.