Scores of convictions for serious crimes may have to be reviewed after a serious blunder by a leading private forensics firm led to a suspected rapist being acquitted, the Guardian has learned.

The company, LGC Forensics, has admitted that a sample at one of its laboratories became so contaminated it could not be offered in evidence.

The rape case, investigated by Greater Manchester police, collapsed this week with the defendant, Adam Scott, 20, who denied the allegation, being acquitted after prosecutors decided they could no longer rely on the forensic evidence. His alleged victim is said to be devastated.

A senior source said: "Potentially this has national implications. Hundreds of cases will have to be reviewed. We have no idea what the parameters will have to be. It's serious – it's dealing with the credibility of the system."

LGC admitted that the sample tying the defendant to the attack had become contaminated with his DNA. It said: "LGC deeply regrets that forensic evidence was contaminated with the defendant's DNA in one of our laboratories.

"LGC has already identified the cause of this contamination, and has taken steps to ensure that it cannot happen again. Our procedure for tracking, identifying and reporting potential contamination will be immediately reviewed and updated. We are also co-operating fully with Greater Manchester police."

LGC refused to answer questions, such as at which lab the contamination had taken place and what exactly caused the contamination.

The senior source pointed out that the cases of most concern were those resting solely or wholly on forensics.

The credibility of LGC and the integrity of its procedures to guard against contamination was central to the conviction of two men for the murder of Stephen Lawrence in January. Gary Dobson and David Norris were convicted predominantly on the basis of forensic evidence from LGC. The trial judge directed that the jury could not consider any other evidence until they were sure they could rule out contamination, which had been the key argument in the defence case.

The case in Manchester that prompted the forensics alert collapsed on Tuesday.

Steve Heywood, assistant chief constable of Greater Manchester police, said: "On Tuesday we were made aware that a DNA profile provided by LGC Forensics in connection with a sexual assault had been contaminated during the testing process in their laboratories.

"The exact circumstances of how the sample was contaminated at the laboratory are yet to be established but I am determined to discover what has occurred. We will work closely with LGC Forensics, the Home Office and other partners to review the full facts of what has taken place.

"In addition we will be conducting an internal review of some investigations where LGC Forensics has been used in the processing of forensic evidence. At this time there is nothing to suggest any other cases within GMP will be affected."

The CPS said it had had no choice but to drop the rape case after it emerged that the forensic evidence had become contaminated in the LGC lab. "The key and significant evidence in the case was scientific evidence linking the defendant to the incident. We were notified earlier this week by Greater Manchester police of further information they had received that the scientific evidence in the original submission could no longer be relied on.

"We have a continuing duty to review cases as they develop and concluded that in view of this new information the prosecution against the defendant should not continue. We immediately informed the court and the defence and offered no evidence. The defendant was formally acquitted of the offence."

Police forces have turned to private suppliers after the government decided to shut down the Forensic Science Service. Its closure was announced in December 2010 by the home secretary, Theresa May, because the government-owned company had been losing £2m a month and was at risk of going into administration.

A Home Office spokesman said: "DNA evidence is a vital tool for the police which has helped convict thousands of violent and dangerous criminals.

"Forensic science regulator Andrew Rennison has launched an immediate investigation to find out what lessons can be learned from this individual case."

LGC has a reputation for leading the way in cutting-edge science and has had success in cold-case reviews, where seemingly dead-end cases result in convictions after fresh forensic techniques produce new evidence.