A draft report about Priti Patel’s conduct concluded in the summer that she broke the rules on ministers’ behaviour, it has been claimed.
A Cabinet Office investigation was launched in March over reports that Ms Patel belittled colleagues and clashed with senior officials in three different departments.
Sir Philip Rutnam, who was the Home Office’s permanent secretary, quit earlier this year accusing Ms Patel of a “vicious and orchestrated briefing campaign” against him.
He added that his decision to resign was with “great regret after a career of 33 years”.
Ms Patel has strongly denied all allegations of bullying.
The report has not been published, but a source told BBC News the report concluded that the "Home Secretary had not met the requirements of the ministerial code to treat civil servants with consideration and respect".
They told the BBC the investigation had found evidence of bullying, even if it had not been intentional.
A second source added that the report was "unambiguous in stating that Priti Patel broke the ministerial code and that the prime minister buried it".
The claims come despite earlier reports investigators “looked at all the claims and found nothing”.
Labour has called on the Government to make the report public as the party said reports that Ms Patel will be issued with a warning were “incredibly serious".
According to reports in the Financial Times, the probe is due to be concluded “imminently” but Boris Johnson is expected to only issue Ms Patel with a written warning, rather than dismissing her from the Cabinet.
Citing unnamed Whitehall officials, the paper said the Prime Minister was intending to “fudge” the outcome of the report which has “robust criticisms” of Ms Patel’s behaviour.
Shadow home secretary Nick Thomas-Symonds said: “Reports that the Home Secretary is to receive a written warning for conduct in government are incredibly serious.
“The role of Home Secretary comes with huge levels of responsibility and trust. It is now vital that the full report is published without delay, so the public can have full confidence in the decision-making process.”
Dave Penman, general secretary of senior civil servants’ union the FDA, said: “In his foreword to the ministerial code, Boris Johnson said: ‘There must be no bullying and no harassment’.
“If, as is being suggested, substance has been found in some of the allegations against the Home Secretary, then the Prime Minister should have no choice but to conclude that the code has been breached.
“As Prime Minister, he is the sole arbiter of the ministerial code but he is also Minister for the Civil Service.
“Having pledged his support for the Home Secretary when the investigation began, and now sat on the report since the summer, he has already undermined confidence in this being a fair and impartial process.”
A spokesman for the home secretary told the BBC she had always denied the allegations and that there had never been any formal complaints made against her.
A government spokesperson said: "The process is ongoing and the prime minister will make any decision on the matter public once the process has concluded."
The Evening Standard has contacted the Home Secretary for any further comment.
