Suella Braverman has been accused of a "cowardly" attack on civil servants after she emailed Tory members slamming officials for blocking policy over small boat crossings.
In a blistering letter to Rishi Sunak, the General Secretary of the FDA union, asked the Home Secretary to withdraw her comments and apologise.
Dave Penman also suggested the Cabinet minister may have breached the ministerial code and risked "stoking tensions" over the issue.
It comes after the Tory party emailed supporters on Wednesday following the announcement of controversial plans for an Illegal Migration Bill.
No10 said the Home Secretary had not seen or signed off the email, which was sent to supporters asking for cash for the Tory party.
The note from 'Suella Braverman' - with her signature at the bottom - read: "We tried to stop boat crossings without changing our laws.
"But an activist blob of left-wing lawyers, civil servants and the Labour Party blocked us."
"So today we're changing our laws - and bringing the small boat crossings to an end," she added.
On Wednesday Mr Penman, the chief of the senior civil servants' union, described the comments as "extraordinary" in his letter to the PM.
He blasted: "Not only is this statement factually incorrect, but the tone of that paragraph and the brigading of civil servants with the Labour Party and 'left-wing lawyers is a direct attack on the integrity and impartiality of the thousands of civil servants who loyally serve the Home Secretary, doing some of the most complex and difficult work in government".
He raised the possibility that Ms Braverman had broken the ministerial code, the rules which govern behaviour of those on the Government front bench.
Mr Penman told the PM: "I am sure I do not need to remind you that paragraph 5.1 of the ministerial code states that 'ministers must uphold the political impartiality of the civil service'.
"I cannot see how the Home Secretary's statement to Conservative Party members can be reconciled with her obligations under the code."
The union chief called for Mr Sunak to ensure the "statement is publicly withdrawn as a matter of urgency" and that Ms Braverman apologises to staff at the Home Office.
Downing Street later said she "did not see, sign off or sanction" an email sent out to Tory members in her name attacking civil servants.
The Prime Minister's press secretary told reporters: "The Home Secretary did not see that email before it went out.
"She did not see, sign off or sanction that email being sent out."
The press secretary suggested there had been an "operational issues" that "we'll have to review" and passed the blame onto Tory bosses.
She was not aware of any "conversations" between CCHQ and Ms Braverman about the incident.
"There would have to be ministerial sign-off usually on things where their name is included on it or it goes out in their name, but I think on this occasion there was obviously operationally the process was not followed."
Conservative Campaign Headquarters later said it is "reviewing" its internal clearance processes, as it admitted Suella Braverman did not see the wording of a widely-criticised email sent in her name.
A spokesperson said: "This was a CCHQ email and the wording wasn't seen by the Home Secretary. We are now reviewing our internal clearance processes."
