It is understood a furious row broke out in No10 about how Mr Johnson was going to respond to the findings of Sir Alex's report, and whether Ms Patel should apologise for her behaviour.
In addition, no feedback was given to the home secretary of the impact of her behaviour, which meant she was unaware of issues that she could otherwise have addressed.
"The Prime Minister is reassured that the Home Secretary is sorry for inadvertently upsetting those whom she was working with but ultimately as the arbiter of the ministerial code, weighing up all the factors, the prime minister doesn't believe there was a breach".
To that extent her behaviour has been in breach of the Ministerial Code, even if unintentionally.
Her approach on occasions has amounted to behaviour that can be described as bullying in terms of the impact felt by individuals.
Dave Penman, general secretary of the FDA senior civil servants' union, told the BBC that civil servants would be asking what message it would send if the government said Patel did not have to resign.
In her statement, Ms Patel said: "I am sorry that my behaviour in the past has upset people".
The Financial Times said that the probe would be concluded "imminently" but that Boris Johnson would only issue Patel with a written warning, rather than dismissing her from the Cabinet.
"I would like to thank the Prime Minister for his support".
"The Prime Minister took advice from independent advisor, Sir Alex Allen, and the Home Secretary has this morning apologised and I would point you towards that apology", the Downing Street spokesperson said.
"If I were prime minister, the home secretary would have been removed from her job".
"The Government should be setting an example". Instead, it is one rule for Boris Johnson and his friends, another for everyone else.
A Government spokesman said: "The process is ongoing and the Prime Minister will make any decision on the matter public once the process has concluded". "Yet when one of his own ministers is found to have bullied their staff he ignores the damning report sat on his desk and instead protects them".
Multiple sources familiar with a draft of the report told the BBC's Laura Kuenssberg that Patel failed to meet requirements of the ministerial code - a government document that sets out rules and standards for United Kingdom ministers.
Allan's long-awaited report on Patel's behaviour was leaked to the Times, the BBC, and other outlets on Thursday following newspaper reports in 2019 that the Home Secretary had been responsible for "bullying, belittling officials in meetings, making unreasonable demands and creating an atmosphere of fear".
Some developing news on the Cabinet Office inquiry, which was launched nine months ago into the conduct of Home Secretary Priti Patel after the resignation of Sir Philip Rutnam, the most senior official in her department.