The Maricopa County Sheriff's Office, which covers the Phoenix region, is also named as a defendant. The office is the target of a federal investigation into alleged discrimination against Hispanics.
"The actions of the sheriff's office are unprecedented. It is unfortunate that the department was forced to resort to litigation to gain access to public documents and facilities," Thomas E. Perez, assistant attorney general for the civil rights division, said in a statement.
Arpaio, a former police officer and Drug Enforcement Administration agent, was first elected sheriff in Maricopa County in 1992. He has become known nationally for aggressive tactics, which have included sweeps looking for illegal immigrants.
The suit was filed in U.S. District Court in Phoenix.
Arpaio said the Justice Department has demonstrated with its lawsuit that its investigators have no evidence of discrimination or racial profiling, The Arizona Republic reported.
"This thing is just camouflage," he said.
The Justice Department has also sued to block enforcement of some parts of Arizona's new immigration law.