The Sunday Times reported claims the home secretary targeted staff and is distrusted by intelligence chiefs, with MI5 officials allegedly withholding information from her.
She has also been accused of trying to force out Sir Philip Rutnam, the most senior civil servant in her department, with the two said to have been involved in “blazing rows”.
The government issued a statement on Sunday night after the claims surfaced, saying it was “deeply concerned” by the “false allegations”, while an ally of Patel’s said the home secretary was “absolutely livid”.
The PM’s official spokesperson said on Monday Johnson backed his minister but refused to be drawn specifically on Putnam.
“The prime minister has full confidence in the home secretary and the vital work that she is doing to make our streets safer and to take back control of the UK’s borders,” the spokesperson said.
But asked whether Johnson had full confidence in the top Home Office civil servant, the spokesperson added: “The prime minister has full confidence in the civil service which is working very hard to deliver on the government’s priorities.”
The Sunday Times claimed the home secretary has not been receiving the same security and intelligence briefings as her predecessors because MI5 officials do not trust her.
A government spokesman said Patel and MI5 had “a strong and close working relationship, and baseless claims to the contrary are both wrong and against the public interest”.
It has been reported that Patel is demanding an inquiry after the reports.
Security minister James Brokenshire, meanwhile, described the reports as “absolute nonsense”.
He said there was “huge frustration” across the Home Office around some of the “false assertions that have been made publicly”.
“I don’t accept those assertions that have been seen in the press about the home secretary,” he told Sky News.
“Yes, she is demanding, but in that role you have to be because you are dealing with some of the most sensitive, some of the most challenging things that you have to deal with across government.
“I think the home secretary is absolutely focused on the public good, the agenda that we’ve set around policing, on immigration and indeed around counter-terrorism and security.”
There are thought to be increasing tensions between the civil service and the government over recruitment and treatment of staff, with the PM’s aide Dominic Cummings thought to be central.
The Cabinet Office is recruiting a new civil servant to oversee HR policy for government ministers’ special advisers.