James O'Sullivan said he was "amazed" that the judge who presided over the priest's manslaughter trial took the case -- because he was a "great friend" of the families involved.
Mr Justice Frank Roe heard the trial in June 1986 shortly after being appointed President of the Circuit Court.
Amid huge controversy, he halted the hearing in less than four hours and ordered the jury to acquit the accused Richard Flynn.
It was the most sensational killing and trial of the 1980s.
In July 1985, the popular Roscommon priest was found battered to death in the Offaly mansion of his socialite friends Therese and Richard Flynn, the day after their daughter's wedding.
The post-mortem concluded that the 52-year-old cleric had been punched and kicked in the head at least five or six times and died as a result of acute brain swelling caused by his injuries.
He did not die instantly but was left for up to six hours after the initial attack before the gardai were called.
Contaminated
The actions of some garda officers in the initial investigation have also been called into question. They allowed vital evidence to be contaminated and many witnesses were never interviewed.
It is widely believed that another individual and not Richard Flynn killed Fr Molloy.
Nearly two years ago, the garda cold case unit launched a new examination following an Irish Independent investigation.
The newspaper produced new evidence that other people were present in the house on the night of the killing.
But the family of Fr Niall said they were deeply disappointed at the slow pace of this probe and are calling on Justice Minister Alan Shatter to establish a commission to answer questions that surround the killing.
Speaking for the first time about the trial, Judge O'Sullivan said: "I was very friendly with Frank Roe. I was amazed at him for taking the case because I always looked on him as a most honourable man. I couldn't believe that he took the case or his actions throughout. He should never have said what he said to the jury. They had no choice but to follow his instructions."