Boris Johnson’s chief adviser should consult civil servants before embarking upon a wholesale programme of Whitehall reform, the head of the senior civil servants’ union has said.

Dave Penman, the head of the FDA union, said a major shake-up of the government machine drawn up by Dominic Cummings without his members’ input could be “reform for reform’s sake” and damage ministers’ ability to implement policy.

Government sources have confirmed reports that Mark Sedwill, the cabinet secretary, is expected to oversee a powerful new business department as part of a slew of expected departmental changes after the UK leaves the EU on 31 January.

The Foreign Office is expected to absorb the Department for International Development to align overseas aid with diplomatic goals. Officials say they could set up a new energy and climate change department.

Stephen Barclay’s Department for Exiting the European Union is expected to be closed down, with responsibility for negotiations over the UK’s future relationship with the EU being led by the Cabinet Office.

Penman said Johnson’s advisers should not get carried away with reforms, which can be expensive and damaging.

“Whilst those around the prime minister may relish in their reputations as revolutionaries sweeping away alleged civil service orthodoxy, reform for reform’s sake is an orthodoxy in itself.

“The civil service is far for perfect, but neither is it dysfunctional. Civil servants will be keen for reform, embracing the challenges the new government faces: that’s why they chose to work in government in the first place.

“Speaking to civil servants to understand what does work and what needs reform is often the biggest challenge for government. The prime minister must now rise to it,” he said.

Cummings, credited with devising the Conservatives’ election strategy that swept Johnson to victory, has been a long-term critic of Whitehall.

In a 2014 lecture, he complained that “almost no one is ever fired” in Whitehall and set out a “to-do list” he had drawn up in case “I ever manage to get control of No 10.”

Sources said Cummings had redrawn those plans during the six weeks of the general election campaign. The plans have been signed off by Johnson with the backing of the Cabinet Office minister, Michael Gove.

Another possible change includes splitting responsibility for the UK’s borders and immigration system off from the Home Office into a standalone department.

Penman, whose members include most departmental permanent secretaries, said that the government should ensure that any potential reforms do not get in the way of policy objectives.

“Ultimately, it is policy that will transform the country, not changing departmental infrastructure. Clarity over objectives and the policies that will deliver them should lead to conclusions on the structures needed to support them, not the other way around,” he said.

The leaders of 115 charities – including Oxfam GB, Unicef UK, WaterAid and World Vision UK – signed a statement amid speculation that Johnson was planning to merge DfID with the FCO.

The sector warned that such a move could lead to less aid reaching those who need it, less transparency about how funds are spent and less efficient use of resources.

Around 30% of the official development assistance budget is now spent outside DfID by other departments and cross-government funds, including the FCO and the Department for Business, Energy and Industrial Strategy.

The charities said a recent report by the Independent Commission for Aid Impact showed this had resulted in less UK aid getting to the world’s poorest people.

The statement reads: “Merging DfID with the Foreign Office would risk dismantling the UK’s leadership on international development and humanitarian aid.

“It suggests we are turning our backs on the world’s poorest people, as well as some of the greatest global challenges of our time: extreme poverty, climate change and conflict.”