Rod Barnes, city manager of Junction City, is resigning amid complaints about the city’s role in handling an anticipated housing boom that hasn’t materialized — a controversy that has led to a Lawrence builder and a former Junction City commissioner being indicted by federal prosecutors.

Barnes, the city’s top administrator for nearly a decade, delivered a letter of resignation Thursday to Mayor Terry Heldstab, who said that he would “reluctantly” accept. The resignation is effective Nov. 1.

Heldstab said Barnes had grown tired of enduring personal attacks regarding the city’s work involving housing developments in the city, which is near Fort Riley.

David Freeman, a Lawrence builder, already has pleaded guilty to federal charges that he conspired to commit bank fraud. He says he funneled $19,000 to Michael “Mick” Wunder, then a Junction City commissioner, to secure permission to build in town.

Wunder also faces federal charges in the case, and an investigation is ongoing.