Gordon Brown will have to devise new ways of handling disputes with Holyrood if the new administration is to be controlled by the Scottish National Party, according to constitutional experts.

Academics have recommended the likely next Prime Minister starts to build formal ways for ministers from the devolved administrations to work with Downing Street and other Whitehall departments.

The Joint Ministerial Committees (JMCs) that were supposed to form a forum for ministers to share ideas and resolve disputes have hardly ever met. The concordats drawn up in 1999, to provide ground rules for handling disputes, have never been tested. And no issue has yet been taken to the legal arbiter, the Law Lords sitting as the Judicial Committee of the Privy Council.

But having different parties in charge in Edinburgh and London, and with the Northern Irish Assembly working again from this week, and following an attack on the Chancellor yesterday for his distribution of new funds to the province, there is growing pressure to change the framework handling disputes between them.

SNP leader Alex Salmond has said he will stake a claim in his first 100 days in office to a share of oil revenue, transfer of some welfare funding and powers to pass gun law.

There are also likely clashes over council tax benefit if the SNP presses ahead with its plans to replace council tax with local income tax.

The Constitution Unit at University College London has proposed regular summits between the UK Prime Minister and heads of devolved administrations.

By meeting regularly, it is argued this could help avert problems and build a stable relationship.

Akash Paun, the academic leading the unit's devolution research programme, said there should also be ways for MPs to meet MSPs, and members of the Welsh Assembly and Northern Ireland Assembly, so they can work their way through policy issues that affect the whole of the UK.

He argued that the means of resolving differences or problems affecting London, Edinburgh and Cardiff over the past eight years is by trying to resolve them at the lowest possible level of the civil service, or through informal ministerial or Labour Party channels.

"Assuming Alex Salmond comes in, the motivations of at least one party changes quite significantly," he said.

Nationalist ministers in St Andrew's House could choose to highlight points of dispute, he said, though it is not always clear they would gain by doing so.

He cited potential clashes over European fisheries negotiations, at which a Nationalist minister could be present, council tax abolition and the question of what happens to £381m per year of council tax benefit, clashes over nuclear power plants or deployment of nuclear weapons.

"The British government has to take a more strategic approach and accept things are going to get more politicised, and should not just wait for trouble to arise but think strategically."

Another contribution to the debate about managing relations between Whitehall and Holyrood comes today from Katie Schmuecker, a research fellow at the Tyneside office of the left-leaning Institute of Public Policy Research.

Writing in The Herald, she suggests a Whitehall shake-up should lead to a Department for the Nations, Local Government and Communities with a full-time cabinet-level minister equipped to deal with co-ordination and conflict.

"The remit would not simply be about managing conflict, it would also be charged with looking at what policies are working effectively in different parts of the UK, and what the home nations can learn from each other," she says.

"The opportunity for such policy learning is one of the great benefits of devolution."