The Recorder of Leeds, Judge Guy Kearl, QC, said he had "considerable concern" over a bulletproof vest which was used as evidence in the case against Denzil Brown Senior.
Former professional boxer Brown Senior, 50, was found not guilty of murdering Christopher Lewis after a five-week trial.
During the trial, Brown Senior claimed he had been "stitched up" when he was questioned about the bulletproof vest which was found in a wardrobe at his home in Morley, Leeds.
West Yorkshire Police have confirmed an investigation will now be conducted by the Professional Standards Directorate.
Mr Lewis, 24, died after being shot in the head outside his home on Reginald Street, Chapeltown, on August 1 last year.
The prosecution claimed Brown got involved in the "execution" of Mr Lewis after his son, Denzil Browne Junior, was seriously injured when he was attacked by members of a rival drug dealing gang called The Flock.During the murder investigation West Yorkshire Police found a bulletproof vest in a bedroom wardrobe at Brown Senior's home
Prosecutors used the discovery as evidence against Brown Senior, claiming the defendant had it for protection as he was living in fear of a revenge attack from members of The Flock.
When Brown Senior gave evidence in the trial, he told jurors he had been issued with the vest more than 20 years earlier by the owner of The Mint Club in Leeds city centre, when he was working there as a bouncer.
Brown Senior said it was given to him for protection when there had been a spate of shootings.
Brown Senior told the court that he stopped working as a doorman at the club on Harrison Street in the late 1990s or early 2000s but had kept the vest as a souvenir.
During cross-examination about the bulletproof vest, prosecuting barrister Dafydd Enoch, QC, asked the court usher to retrieve the vest from the exhibits room and hand it to Brown as he stood in the witness box.
Brown Senior was asked to read aloud what date of manufacture was printed on the label that was attached to the vest.
The label stated 2009.
Mr Enoch said to Brown Senior: "You are lying about that vest. You didn't get that vest when you were working at the Mint Club.
"The vest did not even exist when you were working at The Mint Club."
Brown Senior laughed and replied: "That sticker was not on the vest. Someone has put it on there to try to stitch me up."
The jury of seven men and five women took less than two hours to reach a unanimous not guilty verdict.
After the case, Judge Kearl said he wanted the senior officer in the police investigation and the Crown Prosecution Service to assist in an inquiry.
He said: "I would like there to be an inquiry in to the silver label and how it got on to the bulletproof vest because it raises matters in my mind of considerable concern.
He added: "I will not give any commendations [to police officers involved in the case] until I know what has happened with the silver label and the bulletproof vest."
After the case, a spokesperson for West Yorkshire Police said: "We are aware of the comments made by the judge and the Professional Standards Directorate will commence an investigation in due course."
Two men have already been given life sentences for murdering Mr Lewis.
Gunman Steven Grey and Jonathan Gledhill - who acted as a "stalker" - were convicted of murdering Mr Lewis following a trial in July.Grey was told he must serve a minimum of 32 years in prison. Gledhill was told he must serve a minimum of 31 years behind bars.
Three others - Denzil Browne Junior, Owen Clarke and Lewis Pearce - were found guilty of assisting an offender following the July trial.
Pearce, 27, previously of Sholebroke Street, Chapeltown, Browne Junior, 23, of Oaklands Crescent, Gipton, and Clarke, 26, of Haw Avenue, Yeadon, helped the killers get away from the Chapeltown area afterwards.
They were each jailed for four years.