Priti Patel has told Home Office staff she "deeply values" their work, as fresh bullying allegations against her emerged.
In an internal email seen by the Reuters news agency, Patel expressed "regret" at the decision of her most senior official, Sir Philip Rutnam to resign amid a row over her alleged conduct.
Sir Philip quit as Home Office permanent secretary on Saturday, saying he had been the victim of "a vicious and orchestrated briefing campaign" by allies of the home secretary.
He also claimed that Patel had shouted and sworn at her staff, and accused her of failing to "disassociate herself" from attacks on him.
The top official has vowed to pursue a constructive dismissal case against the Government.
In the email, co-signed by Sir Philip's acting replacement as perm sec Shona Dunn, Patel said: "We both regret Sir Philip’s decision to resign."
And the pair added: "We both deeply value the work that every person in this department does and care about the wellbeing of all our staff. It is therefore a time for us all to come together as one team."
The message to officials comes as new allegations of bullying came to light – but a Conservative party source pushed back and claimed "dark forces" were out to get the home secretary.
The Sun reports that when she was international development secretary, Patel's then-private secretary was "repeatedly harassed and bullied" by her.
According to the paper, the senior official was eventually signed off work with a stress-related illness and asked to be transferred.
The department's then-permanent secretary Sir Mark Lowcock, was reportedly asked to intervene.
However, Patel has dismissed the allegation as “completely false”.
Meanwhile BBC Newsnight reports that Patel was accused by private office staff at DfID of "humiliating" officials in front of others and creating a sense that "everyone is hopeless".
But a Home Office spokesperson said: "The home secretary categorically rejects all of these allegations."
And a Conservative Party source told Newsnight: "What we are seeing is a concerted effort by certain sections of the civil service to undermine a home secretary trying to deliver what people want on crime and immigration.
"It is deeply disturbing that dark forces are trying to influence the findings of a Cabinet Office inquiry."
Patel is currently the subject of a Cabinet Office investigation into whether her she has breached the ministerial code during her time as home secretary.
The FDA civil service union has said the probe has not gone far enough, and has demanded an external layer be brought in to lead the investigation.