According to a regulatory filing by NetApp, the US$128 million settlement relates to an investigation by the US General Services Administration (GSA).
In February, NetApp received a subpoena from the DOJ over the 'over-charging' of Government departments between August 1997 and February 2005, which the DOJ argued was a breach of the U.S. False Claims Act.
The US Government will "release NetApp with respect to the claims alleged in the investigation" as part of the settlement.
"The Agreement reflects neither an admission nor denial by NetApp of any of the claims alleged by the DOJ, and represents a compromise to avoid continued litigation and associated risks," reads the NetApp filing.
Last month, the DOJ also accused NetApp rival EMC of 'improper pricing' in deals made with the US Government close to a decade ago.
IBM, HP and Sun Microsystems have all been embroiled in similar investigations.