The government's top Brexit official, Oliver Robbins, has left the Department for Exiting the European Union and is moving to the Cabinet Office to work more directly for the prime minister.
It is understood there had been tension between him and Brexit Secretary David Davis, the BBC's Laura Kuenssberg said.
She added that the move was also part of Theresa May taking more control of Brexit negotiations.
Mr Robbins will continue to lead the UK officials working on the talks.
The government said the appointment would "strengthen cross-government co-ordination of the next phase of negotiations with the European Union".
It said Mr Robbins would continue to work closely with Mr Davis in his role as the leading "Sherpa" working on talks between UK and EU officials.
Philip Rycroft, currently second permanent secretary at the Brexit department, has been made permanent secretary.
Speaking on BBC Radio 4's The World at One, Lord Kerslake, the former head of the civil service, said he was surprised by Mr Robbins' move and said that the timing was "odd".
"It does feel a bit like rearranging the deckchairs to be honest," he added.
Who is Oliver Robbins?
He cut his teeth at Gordon Brown's Treasury, helping to co-ordinate public spending policy, before going on to serve in senior behind-the-scenes roles for both Tony Blair and Mr Brown in Downing Street. By civil service standards, his rise was meteoric - he was Mr Blair's principal private secretary by the age of 31.
He gained a reputation for being a skilled mediator in the frequent disputes between No 10 and the Treasury.
After a spell as director of the civil service and as David Cameron's deputy national security adviser, Robbins became the senior civil servant in charge of immigration policy at Theresa May's Home Office.
When Mrs May became prime minister she drafted Robbins in as her senior EU adviser.
Mr Robbins is the latest departure from the Brexit department, after the sacking of David Jones and the resignation of Lord Bridges from ministerial roles following the election.
Labour's Brexit spokesman Sir Kier Starmer said: "Moving key individuals at this critical time adds a whole new dimension to the government's chaotic approach to Brexit.
"Deep divisions in the cabinet and a complete lack of leadership are putting the national interest at risk."
Liberal Democrat leader Sir Vince Cable said it was a "sign of the chaos and division at the heart of this government".
The staff changes come ahead of a major speech by Theresa May on Brexit in Florence on Friday - with Foreign Secretary Boris Johnson accused of undermining her by setting out his own vision for life outside the EU in a newspaper article.
Mr Johnson's article triggered a row with the chairman of the UK Statistics Authority over his use of the £350m figure used by the Vote Leave campaign ahead of last year's referendum.