WASHINGTON — Costco Whole­sale Corp. has agreed to an $11.75 million settlement with the Department of Justice over claims that it improperly filled prescriptions for controlled ­substances.

Also under the agreement, the Drug Enforcement Administration over the next three years can make unannounced and unrestricted inspections of all DEA-registered Costco ­pharmacies.

The allegations concerned Costco pharmacies located in Michigan, California and Washington state. Under the settlement, Costco acknowledged that between January 1, 2012, and December 31, 2015, the facilities violated the Controlled ­Substances Act. Violations included filling prescriptions from practitioners without a valid DEA number; incorrectly recording the practitioner’s DEA number; filling scripts outside the scope of a practitioner’s DEA registration; filling scripts lacking all required information; failing to maintain accurate dispensing records; and failing to maintain records for central fill sites in Sacramento, Calif., and Everett, Wash.

DOJ noted that Costco has made improvements in its pharmacies to address issues uncovered in its probe. The warehouse club chain bought a new pharmacy management system for about $127 million and has established a three-tier audit program of its pharmacies.

A company like Costco has “a responsibility to ensure it complies with regulations that help prevent opioids and other dangerous drugs from being misused or otherwise added to the illegal marketplace,” Annette Hayes, U.S. attorney for the Western District of Washington, said in a statement.