The arrest capped a long-running controversy over allegations that beatings, electric shocks and death threats were used against suspects at Burge's Area 2 violent crimes headquarters. The allegations contributed to then-Gov. George Ryan's dramatic decision in early 2003 to empty the state's death row.
Burge, 60, who has long denied wrongdoing, was arrested before dawn at his home in Apollo Beach, Fla., the U.S. attorney's office said. He had moved to Florida after he was fired in 1993.
"There is no place for torture and abuse in a police station," U.S. Attorney Patrick J. Fitzgerald said in a statement. "There is no place for perjury and false statements in federal lawsuits. No person is above the law and no person - even a suspected murderer - is beneath its protection."
Burge attorney James Sotos declined to comment.
The two obstruction counts against Burge each carry a maximum penalty of 20 years in prison, while the perjury count carries up to five years.
The indictment said Burge lied in his response to the civil rights lawsuit when he said he and other detectives hadn't tortured anyone.
That lawsuit, filed by Madison Hobley, alleged that Burge and other detectives had tortured him, including covering his head with a typewriter cover until he couldn't breathe in 1987.
Hobley was suspected of setting a fire that killed seven people including his wife and son. Hobley says he never did confess and that a confession introduced at his trial was fabricated by homicide detectives.
He was convicted in 1990 and spent 13 years on death row but was among four men pardoned by Ryan in January 2003. The other 167 people then on Illinois' death row had their sentences commuted by Ryan, in most cases to life in prison.
An attorney who represents other two men allegedly tortured by Burge's detectives called the arrest of "enormous symbolic importance" in Chicago, where the police department has long been dogged by allegations of misconduct.
"This has been a symbol of a pattern of racism and of police as an occupier in certain neighborhoods, and the federal government stepping in here just has enormous importance even if it only this one case," said Locke Bowman, of the MacArthur Justice Center at the Northwestern University School of Law.
A report by two special prosecutors appointed by the Cook County Circuit Court concluded two years ago that Chicago police beat, kicked, shocked or otherwise tortured scores of black suspects in the 1970s and 1980s as they tried to force confessions. But they said the actions were too old to warrant indictments.
The city has more recently agreed to pay $20 million to settle lawsuits by Hobley and other former inmates.
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