The lawsuit calls Arpaio and his office's defiance "unprecedented," and said the federal government has been trying since March 2009 to get officials to comply with its probe of alleged discrimination, unconstitutional searches and seizures, and having English-only policies in his jails that discriminates against people with limited English skills.
Arpaio had been given until Aug. 17 to hand over documents it first asked for 15 months ago.
Arpaio's attorney, Robert Driscoll, declined immediate comment on the lawsuit, saying he had just received it and hadn't yet conferred with his client.
Arpaio's office had said it has fully cooperated in the jail inquiry but won't hand over additional documents into the examination of the alleged unconstitutional searches because federal authorities haven't said exactly what they were investigating.
It's the latest action against Arizona by the federal government, which earlier sued the state to stop its strict new immigration law that requires police officers to question people about their immigration status.
"The actions of the sheriff's office are unprecedented," said Thomas Perez, assistant attorney general for the department's civil rights division. "It is unfortunate that the department was forced to resort to litigation to gain access to public documents and facilities."
The lawsuit was filed in U.S. District Court in Phoenix and names Arpaio, the Maricopa County Sheriff's Office and the county.
Arizona's new law most of which a federal judge has put on hold mirrors many of the policies Arpaio has put into place in the greater Phoenix area, where he set up a hot line for the public to report immigration violations, conducts crime and immigration sweeps in heavily Latino neighborhoods and frequently raids workplaces for people in the U.S. illegally.
Arpaio believes the inquiry is focused on his immigration sweeps, patrols where deputies flood an area of a city in some cases heavily Latino areas to seek out traffic violators and arrest other offenders.
Critics say his deputies pull people over for minor traffic infractions because of the color of their skin so they can ask them for their proof of citizenship.
Arpaio denies allegations of racial profiling, saying people are stopped if deputies have probable cause to believe they've committed crimes and that it's only afterward that deputies find many of them are illegal immigrants.
The sheriff's office has said half of the 1,032 people arrested in the sweeps have been illegal immigrants.
Last year, the federal government stripped Arpaio of his special power to enforce federal immigration law. The sheriff continued his sweeps through the enforcement of state immigration laws.
Last year, the nearly $113 million that the county received from the federal government accounted for about 5 percent of the county's $2 billion budget. Arpaio's office said it receives $3 million to $4 million each year in federal funds.
In a separate investigation, a federal grand jury in Phoenix is examining allegations that Arpaio has abused his powers with actions such as intimidating county workers by showing up at their homes at nights and on weekends.