Less than 10% of police forces have met basic quality standards for fingerprint evidence, the government’s forensic science regulator has warned.

All UK forces were ordered three years ago to ensure their laboratories met international standards for analysing prints found at crime scenes. But only three forces have complied, with almost every force missing a deadline set by the regulator to gain accreditation by November.

Police forces that have failed to obtain accreditation, which include the Metropolitan police and Greater Manchester police, will have to declare this in court, prompting concerns that cases could collapse as a result of unreliable evidence.

Gillian Tully, the government’s forensic regulator, said: “The shortcomings identified do not mean that all fingerprint evidence is of poor quality, but they do highlight risks to the quality of evidence.

“The risks are greatest in situations where the comparison is complex, for example because the fingermark is partial or distorted.”

The National Police Chiefs’ Council lead for forensics, Ch Const James Vaughan, said: “We are treating delays in in gaining accreditation as a critical incident, with a chief officer overseeing forces’ progress and assisting them in gaining accreditation as soon as possible.”

The failures are the latest problems to have affected forensics in the past year. Alleged data tampering at Randox Laboratories in Manchester led to dozens of criminal convictions being overturned and required thousands of samples to be reanalysed.

Problems in digital forensics caused the collapse of a number of rape trials and police were criticised for outsourcing digital work to unaccredited private labs that are subject to no regulatory oversight.

In a recent submission to a House of Lords inquiry, the Leverhulme Research Centre for Forensic Science raised broader concerns about the way fingerprints, tool marks, footwear, tyre marks and ballistics evidence were being used in courts.

Prof Niamh Nic Daéid, the centre’s director, said: “The majority, if not all of those techniques, are not robustly researched. In a lot of cases, the comparative process is left to the subjective opinion of the person doing the comparison. It often could be described as no better than spot the difference.”

She said more rigorous research was needed on error rates associated with this type of evidence.

In her submission to the same inquiry, Tully said there had been a resistance in fingerprint evidence to move away from the traditional approach of an expert declaring an identification towards a more transparent, scientific approach, with objective measures and an acknowledgement of the possibility of false matches.

Vaughan said forces that had failed to meet official standards had been asked to consider outsourcing work to existing accredited labs, and that they would be open in providing declarations to court if analysis was carried out at unaccredited facilities.

“It is then for the court to test the veracity and admissibility of the evidence and, to date, no concerns raised have been raised by courts,” he said.