The United Kingdom’s unity faces being destabilised by “flag-waving unionism” from English nationalist politicians, one of the most senior officials to emerge from Northern Ireland’s traditionally Catholic community has warned.

Ciaran Martin, who created the framework for Scotland’s 2014 independence poll as the Cabinet Office’s constitution director, said the “complex identities” of Northern Ireland faced being undermined by post-Brexit attempts to “redesign” the British state based on “a narrow 17th-century notion of English sovereignty”.

While Boris Johnson had said in Belfast in March that there had to be broad acceptance of governing arrangements from those who were not part of the majority there, rather than a 50% plus one majority for the union, “what we have from London instead is England-first, flag-waving politics and policies,” Martin said.

This was “Greater Englandism”, he added. “But it’s not a unionism of partnership. It’s a unionism where England sets the rules because that’s enough for a governing majority. If Scotland doesn’t like it, it gets overruled or ignored. If Northern Ireland doesn’t like it, it gets told nothing’s really changed but here are some special, highly destabilising arrangements to make sure you don’t mess things up for England.

“It’s astounding just how fast the idea and practice of the UK as a partnership seems to be declining.”

Speaking openly but carefully for the first time about his own feelings on the subject as Northern Ireland prepared to commemorate its centenary on Monday, he said the border issue had been talked up but what had been overlooked was the “dramatic removal of the acceptance and appreciation” of subtleties of national identities where he had grown up.

The common European identity, for example, had been “seriously important in terms of softening feelings the minority community,” said Martin, who held senior Cabinet Office roles between 2005 and 2013 before heading the first National Cyber Security Centre.

He said in an interview with the Guardian that Northern Ireland faced for the first time its history a crisis that had come from outside of it.

“What sort of UK is the government building and what is Northern Ireland’s place in it? Because at the moment it seems that the UK government wants to build a post-Brexit UK based on a very 17th-century English notion of parliamentary sovereignty. It was delivered with English and Welsh votes but we are talking about a very singular sense of identity rooted in the English tradition.

“There has been a dramatic removal of the acceptance and appreciation of the subtleties of national identities within the United Kingdom, particularly in Northern Ireland at a time when identity there is becoming much more complicated,” he said, adding that the forthcoming census results were likely to be fascinating.

“So we have a highly nuanced position in Northern Ireland, and yet we have now got a redesign of the British state based on an incredibly English version of national identity, which is probably one of the most unhelpful developments that could have happened to Northern Ireland.”

There had been no acceptance on the part of the British government that Brexit had been highly disruptive to both communities, he said. “The government has a general duty to promote stability in Northern Ireland. You can undermine the delicate political and social balance in Northern Ireland without breaching the letter of the 1998 Good Friday agreement.”

Martin, who now lectures at the University of Oxford’s Blavatnik School of Government, said there was a “fundamental lack of seriousness and lack of purpose” in relation to Northern Ireland, and the politics behind it had been driven much more by Brexit than Northern Ireland’s needs.

Martin said he feared that the path he had followed into the Whitehall civil service might now look a lot less attractive to younger people from his background.

“When I went into government in the early Blair years, there was a lot of optimism and a huge amount of effort going into making the post-conflict, newly devolved UK work,” he said. “What’s being built now and how does that relate to the communities in Northern Ireland?”