Nuri al-Maliki's media office said the trial was like the offering condolences for the victim's families because they could see the "dictator being tried for the crimes and massacres he had done".
"Saddam and his co-defendants are standing before court to be tried for the al-Anfal massacres committed against our Kurdish people between 1987 and 1988... Tens of thousands of them were buried in mass graves for nothing just because they were Kurds.
"The former regime's record is full of crimes that were even more savage than those committed by Nazis and fascists in world war two. The regime's crimes hit every sect in the Iraqi people," the statement said.
Attack on justice
But Dr Fadil al-Rubei, an Iraqi politician, the former opponent of the deposed president and a member of Iraqi National Alliance party said the statement was an attack on justice.
"The statement has resubmitted the old question on whether or not this court enjoys any legitimacy," he said.
"The trial proves that the Iraqi judiciary in its worst days; a court set up by the political opponents of a certain person and trying him for acts that happened 20 years before their court's law was written.
"It is revenge on a political opponent, not more than that."
Most of current Iraqi government members belong to political parties that are considered the fiercest opponents to Saddam's Baath party.
Al-Maliki belongs to al-Dawa party which took arms against the Baghdad government in the 1970s and 1980s. Its senior members escaped to Iran after a massive crackdown in 1980.
Al-Rubei said: "They want to get revenge against Saddam Hussein because his rule prevented them for decades from doing what they are doing in Iraq today.
"And both Iraq's rulers and the US want this trial to end quickly before starting their withdrawal from Iraq."
Fadil Karim, a member of the Patriotic Union of Kurdistan (PUK) led by Jalal Talabani, the current Iraqi president, said he sees nothing wrong in the statement.
"I cannot see how the statement is some kind of interference or pressure on judges. There is no executive body in Iraq with the power or the authority to steer the court to a certain direction."
Saddam and his cousin, Ali Hasan al-Majid, a Baath party leader who allegedly organised Anfal, are charged with genocide - considered the toughest charge to prove since it requires showing that their intention was to exterminate part of an ethnic group.
Saddam and al-Majid also face charges of crimes against humanity and war crimes, as do their co-defendants, most of whom are former military figures.
Saddam is still awaiting a verdict in the first case against him, the killing of 148 Shia in al-Dujail in the 1980s. In that case as well, he and seven other co-defendants may face the death penalty.
Lawyer's office attacked
In a separate development, Badee Izzat Aref, a lawyer for one of Saddam Hussein's co-defendants in the Anfal trial, said his office had been attacked by people claiming to be members of a Shia Iraqi political party.
Aref said the intruders, who said they were from the Supreme Council for the Islamic Revolution in Iraq, took away computers and papers and threatened his secretary at gunpoint demanding to know the whereabouts of Aref.
However, Aref, who is also the defence lawyer for Tariq Aziz, suggested the men were impostors.
He said: "It is unlikely that the group belongs to the Supreme Council for the Islamic Revolution."
Aref said he linked the act, which took place on Wednesday, to his performance in the trial and that it was one in a series of such attacks.
In October 2005, Sadoun Nasouaf al-Janabi, a lawyer who was defending an associate of Saddam Hussein, was seized by armed men at his office in Baghdad and later shot in the head.