The death of one of the Western Cape's top urban terror police investigators four years ago remains unsolved after the acquittal on Tuesday of two men charged with his murder.

Bennie Lategan was investigating an explosion in the parking area at the V&A Waterfront when he was gunned down on the corner of the R300 and Vanguard Drive on January 14, 1999.

Pagad members Ebrahim Jeneker and Ismail Edwards were arrested on the R300 highway a few days later and charged with his murder and related charges, including the possession of unlicensed firearms and ammunition and malicious damage to property.

They pleaded not guilty and were acquitted of all charges in the Cape High Court.

The state contended that the men robbed Lydia Isaacs of a blue Toyota Corolla at gunpoint in Lansdowne on January 9, 1999, drove off in the vehicle and days later used it to chase Lategan, who was in his car, and that they then shot him 13 times.

The car was set alight in Athlone Industria later that day.

In her judgment on Tuesday, Acting Judge Cecile Williams questioned the state's investigation of the evidence of a 13-year-old street child who told the court he had witnessed the murder and identified the two men as Lategan's killers. The child said he had been begging at the intersection where Lategan had given him money.

But the judge asked why investigators had waited for four months after the murder before they took his statement. She also said the child had mentioned Edwards's "lazy eye" to police but not in his statement. It seemed to her, she said, that Jeneker was the state's only suspect and that they had gone about building a case against him.

The judge said the argument of state advocate Eunice van Wyk that Edwards's alibi that he had gone to a mosque because it was a holy day on the Muslim calendar was weak and the state did not provide the court with expert testimony to contest the alibi. She said she therefore had no choice but to acquit the accused on all charges.

Jeneker is serving three life sentences and 116 years for multiple urban terror-related charges.

Edwards is serving 25 years for a pipe-bomb attack on the Lansdowne police station in January 1998.