Another was issued for his uncle Ahmed Chalabi, the founder of the Iraqi National Congress and a former key ally of the US. He is accused of money laundering.
Both men denied the accusations, which they said were politically motivated.
Salem Chalabi, head of the Iraqi Special Tribunal, was named as a suspect for the murder in June of Haithem Fadhil, director general of the finance ministry.
Last night he said the allegations were designed to interfere with preparations for the trial of senior officials of the former regime.
If convicted he could face the death penalty, which was restored by the Iraqi interim government yesterday.
It was unclear last night what impact the warrant would have on the trials of Saddam and other officials of his former regime.
Salem Chalabi, who is in London, said in February he thought it could be two years before Saddam appeared in court.
The US has handed Saddam over to the Iraqis for trial.
“The warrant for me has to do with the fact that apparently I threatened somebody. I have no recollection of ever meeting that person, but apparently I threatened somebody who subsequently was killed,” he told CNN.
“I don’t think that I had anything to do with the charges so I’m not actually worried about it. It’s a ridiculous charge, that I threatened somebody. There’s no proof there.”
Iraq’s senior investigative judge, Zuhair al-Maliky, said that nobody in Iraq should enjoy immunity. “They should be arrested and then questioned and then we will evaluate the evidence, and then if there is enough evidence, they will be sent to trial.”
Ahmed Chalabi is accused of counterfeiting Iraqi dinars removed from circulation after Saddam’s regime fell. The fake money was allegedly found in his house.