The chair of the Criminal Cases Review Commission has rejected calls from the justice secretary to resign after a report on its handling of the Andrew Malkinson case laid bare “a catalogue of failures”.

A review by Chris Henley KC found that Malkinson, who spent 17 years in jail for a 2003 stranger rape he did not commit, could have been exonerated almost a decade earlier. It also contained personal criticism of the watchdog’s chair, Helen Pitcher, for failing to apologise and for “taking too little responsibility”.

The new justice secretary, Shabana Mahmood, said Pitcher was “unfit to fulfil her duties” and that she was seeking her removal in light of the findings. It is understood that she made her position clear to Pitcher on Thursday morning in the hope that she would resign.

But Pitcher said she was the “best person” for the job and that she had no intention of standing down. She also said that with hindsight she would have apologised sooner, and that the CCRC had told her not to.

Pitcher said: “I have been credited by the MoJ for substantially turning the CCRC round … I honestly believe I am the best person to take this forward for as long as I have the opportunity to do so.”

Because the CCRC is an independent body, unless Pitcher resigns she can only be removed from her post by the king, acting on the recommendations of a panel. This will now be convened.

Mahmood said: “It was sobering to read Chris Henley KC’s findings. My thoughts are with both Andrew Malkinson and the victim of this horrific crime. Having studied Chris Henley’s report closely, it is my firm view that Helen Pitcher is unfit to fulfil her duties as chair of the CCRC. I have therefore begun the process to seek her removal from that position.”

The CCRC is the gatekeeper to any case being reconsidered by the court of appeal in England, Wales and Northern Ireland and is tasked with investigating miscarriages of justice.

Case files show that even in 2022 it was minded to turn down Malkinson’s latest appeal if an alternative suspect was not found, which Henley said showed it was still taking “too cautious an approach”, which needed “urgently to change”.

Henley said the discovery in 2007 of searchable male DNA on the victim’s vest that did not belong to Malkinson was “not properly understood” by the CCRC. There was never any DNA linking Malkinson to the crime and the report said staff needed more training to make sure they understood forensics.

Writing for the Guardian, Malkinson said the discovery of how close his case had come to being refused in 2022 “shook me to my core”. It was this application that led to his conviction being overturned in 2023.

“I did not believe I could get any angrier about what has been done to me, but reading Mr Henley’s findings incensed me,” he wrote. “The truth is that there is something deeply wrong at the CCRC and nothing less than a complete overhaul is needed.”

Malkinson applied three times to the body before it made a referral to the court of appeal. The CCRC did not examine the original police file in any of the three applications and only conducted further forensic testing in the final application after his lawyers showed it the results of their own tests.

Malkinson said he was encouraged that the justice secretary wanted Pitcher to go. “Pitcher and her discredited and incompetent senior leadership team should now be replaced with people with a track record of fighting injustice without fear or favour. Survivors of wrongful conviction like me and the sub-postmasters should have input into the recruitment process,” he said.

The CCRC was keen to highlight Henley’s observation that his findings were “necessarily limited to” Malkinson’s case. However, Henley told the Guardian that “it would be worryingly complacent simply to pass this off as an isolated case”. He said: “Since delivery of the first draft of my report at the end of January, neither the chair nor chief executive has asked to speak to me about my findings.”

Pitcher faced repeated calls to apologise and hand back her OBE when Malkinson was exonerated last summer, given the part the CCRC had played in prolonging his time in jail.

Henley said criticism of the organisation’s “failure to apologise” last year was “well founded”. He wrote: “There should be a wholehearted apology made by the CCRC to Mr Malkinson. The CCRC failed him.”

Pitcher issued an “unreserved apology” only in April when she received the final report, which included Henley’s blunt demand that she say sorry. Henley also said Pitcher had “claimed too much credit” for Malkinson’s exoneration and “took too little responsibility for the mistakes” in statements released last year.

Pitcher said: “It was a mistake with hindsight not to apologise sooner. It should have been done and at a human level I would have done it. At a corporate level there was a view that I shouldn’t until the investigation was concluded.”

Pitcher did not appear in broadcast interviews on Thursday. She said she offered to do them from home despite recovering from an operation earlier this week but was told by the CCRC it “would not be advisable”.

In Malkinson’s most recent application to the CCRC, his team at the legal charity Appeal uncovered significant new evidence pointing to his innocence, including significant disclosure failures and more forensic evidence. The court of appeal later concluded that the disclosure failings alone would have made his conviction unsafe.

James Burley, who led Appeal’s investigation into Malkinson’s case, said the report was “utterly damning” and detailed “a catalogue of failures by the CCRC”.

He said: “No one can doubt now that the CCRC is a broken safety net which sets the bar unreasonably high for innocent prisoners trying to clear their names. The CCRC must be completely overhauled.”

Henley said the case “demonstrates a deep-seated, system-wide, cultural reluctance, which starts right at the top in the court of appeal, to acknowledge our criminal justice system will on occasion make mistakes, that entirely innocent defendants will sometimes be convicted, and have this possibility at the forefront of our collective mind when trying and reviewing cases”.

Henley also said the CCRC was in urgent need of more resources because of the “formidable challenges” it faced, including a significant rise in applications and a real-terms decline in budget. In 2023-24 it received a record 1,629 applications and has it asked for a 15% budget increase.

Responding to the report, the CCRC said it would “learn from the mistakes that were made” and that work to address Henley’s recommendations had already started.

It said: “We have referred 839 cases for appeal, and the court of appeal criminal division has often commended our investigative work and analysis … Against that background, we deeply regret that our analysis and handling of Mr Malkinson’s case did not meet the standards we set for ourselves and which applicants are entitled to expect, and we offer our wholehearted and unreserved apologies to Mr Malkinson.”