The report is based on 10 months of observation and dozens of interviews with judges, prosecutors and defence lawyers.
It says the court that tried Saddam and seven co-defendants "was undermined from the outset by Iraqi government actions that threatened the independence and perceived impartiality of the court".
"[The court] was undermined by Iraqi government actions that threatened the independence and perceived impartiality of the court"
Human Rights Watch
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"Unless the Iraqi government allows experienced international judges and lawyers to participate directly, it's unlikely the court can fairly conduct other trials," the report said.
Saddam was sentenced earlier this month after a trial lasting more than a year for his role in ordering the deaths of 148 Shia civilians from the town of Dujail, north of Baghdad, after an assassination attempt in 1982.
The verdict and sentences in the first trial are currently under appeal.
The former Iraqi president, who was sentenced to death by hanging along with two other defendants, is now on trial for genocide.
European governments have led calls for the death sentence against Saddam to be commuted while George Bush, the US president, described the conviction and sentence as "a major achievement" for Iraq.