Taha Yassin Ramadan, Iraq's former vice-president, was hanged before dawn on Tuesday for his role in the killing of 148 Shia Iraqis in Dujail, an official in the prime minister's office said.
"Ramadan was hanged at 3:05am today," said the official who witnessed the hanging.
No official announcement has been made by the government.
The official said Ramadan was weighed before the hanging and the length of rope was chosen accordingly to prevent a repeat of what happened to Barzan Ibrahim al-Tikriti, Saddam Hussein's half brother and former intelligence chief, who was decapitated on the gallows.
Ramadan was convicted in November of murder, forced deportation and torture, and sentenced to life in prison.
A month later, an appeals court said the sentence was too lenient, and returned his case to the High Tribunal, demanding he be sentenced to death.
The court agreed to turn it to a death sentence last week.
Ramadan is the third Saddam aide to be hanged for crimes against humanity since the former government was ousted by US-led forces four years ago.
Ramadan's son, Ahmed, denounced the execution.
"It was not an execution. It was a political assassination," he told Al Jazeera by telephone from the Yemeni capital Sanaa.
He said a family representative had attended the execution and that his father's body would be buried in Tikrit, north Baghdad.
Saddam was hanged for the Dujail killings on December 30 while al-Tikriti and Awad Ahmed al-Bandar, the former head of the Revolutionary Court, were executed on January 15.
The executions have outraged Iraqi Sunnis and caused concern among international human rights groups, which had appealed for Ramadan's life.
Ramadan had maintained his innocence, saying his duties were limited to economic affairs, not security issues.
Human Rights Watch and the International Centre for Transitional Justice have said the evidence against him was insufficient for the death penalty.
Agencies
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