Prosecutors dropped the case, investigated by Greater Manchester Police, after a potential piece of evidence became contaminated with the defendant's DNA in a laboratory run by LGC Forensics.
The Home Office said forensic science regulator Andrew Rennison had launched an immediate investigation.
Steve Heywood, assistant chief constable of GMP, said the force would be conducting an internal review "of some investigations where LGC Forensics has been used in the processing of forensic evidence" but that there was "nothing to suggest any other cases within GMP will be affected".
A senior source told the Guardian: "Potentially this has national implications. Hundreds of cases will have to be reviewed."
LGC told the newspaper it "deeply regrets" the incident, and had identified the cause of the contamination and taken steps to ensure it could not happen again.
The Crown Prosecution Service said it dropped the case after it was informed by the police that the evidence "could no longer be relied upon".
"We immediately informed the court and the defence and offered no evidence. The defendant was formally acquitted of the offence."
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."