Criticism of the Metropolitan Police’s approach to tackling corruption within its ranks is “alarming”, the policing minister has told MPs.

A watchdog’s findings that the force’s procedures for rooting out corrupt officers and staff were “fundamentally flawed” and “not fit for purpose” were “troubling”, Kit Malthouse said.

The Met had not learned lessons from the notorious unsolved 1987 murder of private investigator Daniel Morgan and had a “degree of indifference” to the risks of corruption, according to damning conclusions published on Tuesday by Her Majesty’s Inspectorate of Constabulary and Fire and Rescue Services (HMICFRS).

Inspectors were called in by the Home Secretary after an independent inquiry into how the force handled Mr Morgan’s case found it was institutionally corrupt, saying it had concealed or denied failings to protect its reputation.

Speaking in the Commons on Wednesday, Mr Malthouse said he wanted to “note at the outset” that there were “some positive findings” but added: “The broad thrust and overarching conclusions of the report are troubling.

“This inspection was commissioned to provide assurance for Daniel Morgan’s family and the wider public that the force had learned from failings of the past and had robust arrangements in place to prevent, identify and tackle corruption in its ranks.

“I’m afraid it is deeply disappointing, but in the light of the findings of this report, I cannot provide this assurance to the House.

“Indeed, the inspectorate felt that the Metropolitan Police’s approach suggested, and I quote, ‘a degree of indifference to the risk of corruption’. This is alarming.”

Among the findings, the report said that more than 2,000 warrant cards issued to personnel who had since left the force were unaccounted for.

Mr Malthouse told MPs: “This is particularly concerning coming as it does just over a year after a police officer abused his position to murder a young woman in a heinous crime that shocked our country to its core.”

Met constable Wayne Couzens used his valid warrant card to kidnap Sarah Everard before he raped and murdered her in March last year.

The report “comes at a time when the Metropolitan Police is under intense scrutiny”, Mr Malthouse said, adding: “I have found myself at the despatch box discussing the force’s culture and standards all too frequently in recent months.

“As someone who over the years worked alongside the Met and (has) seen first-hand the incredible things that that organisation is capable of achieving, I know that there are thousands of officers, staff and volunteers across the organisation who perform their duties with skill, professionalism and pride every day.

“However, when things go wrong, it is vital to acknowledge that fact and take every necessary step to make sure the failings of the past are not repeated.”

He told MPs the Home Secretary Priti Patel had written to the Met Commissioner and the Mayor of London to “set out her expectation that they respond to her with a clear action plan to remedy these failings”.

Placing “particular emphasis” on the role of the mayor, he said: “It is incumbent on City Hall to be holding the Met Police leadership to account for responding to past failures.

“This clearly hasn’t happened. And I urge the mayor to work with the Home Office to ensure a new commissioner can address these failings.”

On Tuesday, Mayor of London Sadiq Khan branded the findings “deeply worrying” and said: “It is crystal clear to me that action needs to be taken at the highest levels of the Met in order to regain the trust and confidence of Londoners.”

Shadow policing minister Sarah Jones said the report “lays bare real issues of concern”, telling the Commons: “The outgoing commissioner must begin the process of implementation, but this must be a top priority for the new commissioner who will carry forward this work. But the issues raised have national consequences. The Home Office must not stand back, real leadership is needed.”

She said Labour had called for an “overhaul of police standards”, including reviews of vetting, training, misconduct proceedings and use of social media.