General manager Billy King said the center should be ready for training camp in the fall.
The surgery was performed by Nets team orthopedic Dr. Riley Williams III and Dr. Andrew Weiland at the Hospital for Special Surgery.
"Brook was bothered this year by a bony lump that developed after he was hit in the arm early this year," Williams said. "The mass was successfully removed today. A full recovery is expected, and Brook should be able to return to basketball activities in approximately six weeks."
The team release did not define a "bone mass," but a team spokesman said it was not related to cancer.
Lopez, who has never missed a game due to injury in his three-year career, averaged a team-high 20.4 points and 6.0 rebounds this past season.