Crime and Corruption Commission presiding officer Forbes Smith applied to a Queensland court for the man, who is not named in a published judgment, to be punished for contempt after he refused to testify about his involvement in "some suspicious behaviour".
The man was shot in the back in June last year, but was able to call triple zero and avoided death by being taken to hospital for surgery.
In dismissing the CCC's application, Brisbane Supreme Court Justice Jean Dalton said there is evidence of "real danger to his life" had he answered the watchdog's questions.
She also questioned why police affidavits objecting to bail for the two people accused of attempted murder over the shooting were not put before the CCC's presiding officer or her court by the commission.
"It was not fair for the CCC to argue that the respondent only put before the Court mere assertion and no evidence of a real threat, when it knew that the objection to bail affidavits supported a very different picture and it did not put them before this Court," she added.
Justice Dalton said the victim was referred to by the CCC as "uniquely placed" to provide information, suggesting it was likely the offenders, or their associates, would realise the source if police acted.
The man was ordered to attend a CCC hearing in September, where he was required by law to answer questions unless he had a reasonable excuse.
After some preliminary questions, his lawyer objected to a question about the suspicious behaviour saying he had a reasonable excuse not to answer.
Asked again, the man said he was unwilling to answer as he was "scared for my life".
During later proceedings he also refused to respond saying he was afraid of retribution.
"I'm scared for my life that the people that shot me are going to take my life because youse has brought me here to testify against them," he told the CCC hearing.
But the presiding officer refused to discharge him, saying he was in contempt of the CCC.
Justice Dalton said the seriousness of the attack was known by the time of the hearing as two men had been arrested.
She said objection to bail affidavits showed there was an objective basis for his fears as the men - and their associates - were dangerous and violent.
She referred to police material stating the shooting appeared to be an unprovoked and premeditated attack, and the victim had not co-operated with officers likely due to the capacity of the men and associates to commit acts of serious violence.
One man was described as extremely violent and volatile and having no regard for human life or the consequences of his actions.
Police also voiced a grave concern for the victim's safety should the men be released from custody and serious concerns retribution will be sought if it appears the victim was speaking to officers.
Justice Dalton said she could see difficulties when the CCC is represented by in-house lawyers on such an application as the CCC is complainant and prosecutor.
The CCC's counsel said he regarded himself as "being bound by an overriding duty of fairness" in prosecuting the contempt application.
But Justice Dalton could not see that the commission or its counsel "acted consistently with this duty".
