The outgoing Metropolitan Police commissioner has warned against the “politicisation of policing”, saying this is “a threat not just to policing but to trust in the whole criminal justice system”.

Making some final remarks before the end of her tenure, Dame Cressida Dick described police operational independence from government as “crucial” in what may be seen as a swipe at political leaders in the wake of her downfall.

She quit after London mayor Sadiq Khan criticised her handling of racist, misogynist and homophobic messages shared by a group of officers based at Charing Cross police station and after a series of other scandals which have plagued the Met during her time in post.

Her resignation was met with dismay by staff and came just hours after she said in an interview that she had no intention of quitting.

On Friday, a smiling Dame Cressida was cheered and applauded by a large crowd of police officers and staff bidding her an emotional farewell outside Scotland yard, ahead of her last day on the job this weekend.

Meanwhile, Mr Khan said he was not “going to hide from the fact” that he lost confidence in her.

In a “letter to London”, Dame Cressida wrote: “Of course as I look back there is more I wish we had achieved.

“We hear the criticism, know not everyone has confidence in us to provide a good service when they need us, and have seen among us those whose horrific actions have let you all, and us, down so terribly.

“Each one drives us to get better, to root out those who don’t uphold our standards and don’t deserve to wear our uniform… We are listening and acting on what you tell us so we can change for the better.

“The current politicisation of policing is a threat not just to policing but to trust in the whole criminal justice system. Operational independence from local and central government is crucial for an effective democracy and is a model respected around the world. We must all treasure and protect it.”

Speaking at the launch of Labour’s local election campaign in Barnet, north London, Mr Khan said: “In the recent past, she’s worked with many others to help us reduce violent crime but I’m not going to hide from the fact that I lost confidence in her.

“I’m not going to hide from the fact that we’ve had in our city a series of devastating scandals, overt racism, sexism, discrimination, homophobia, we’ve had trust and confidence from Londoners in the police service at rock bottom.

“It’s one of the reasons why I lost confidence in her and it’s one of the things I’ll be looking for in a new commissioner, how they will address some of these serious issues that, frankly speaking, the current commissioner failed to address.”

Dame Cressida was met with cheers of “hip, hip, hooray” and saluted by a guard of honour as she waved and thanked those who had gathered for her send-off.

During an earlier visit to the Metropolitan Police Specialist Training Centre in Gravesend, Kent, she reiterated that the mayor “caused me to say that I would step aside” and that she did not “voluntarily resign” – the circumstances of which are being reviewed by outgoing chief inspector of constabulary, Sir Thomas Winsor.

Dame Cressida told reporters the culture in the force “has been changing”, adding: “I believe during my commissionership you have seen a real opening up of the Met.”

Two inquiries are under way looking at the culture within the Met in the wake of the murder of Sarah Everard by then-serving police officer Wayne Couzens, the jailing of two officers who took pictures of the bodies of murdered sisters Bibaa Henry and Nicole Smallman, criticism of how the force handled the partygate scandal and the Daniel Morgan report which blasted the Met’s failure to tackle corruption.

Dame Cressida leaves as more than 34,000 officers are employed at the Met, the highest in history according to the force which is almost 200 years old.

She reviewed 157 police constables and 25 detective constables as she led her last ever passing out at Hendon in north-west London.

Dame Cressida said she would “always look back on my time as commissioner with pride for what has been achieved, with humility for when Londoners have been let down, and with huge confidence the changes we have been making will ensure you can be proud of the Met going forward”.

Her last day in post will be on Sunday, after which she will take unused annual leave, with her final day of employment being April 24.

Deputy commissioner Sir Stephen House will temporarily serve as acting commissioner while the recruitment process continues.

This could take around five months, Mr Khan said, adding that the best candidate would be “somebody who understands the challenges we face and also recognises the uniqueness of London”.