JPMorgan Chase & Co. must continue to defend against Labor Department claims that the company discriminated against female technology employees by paying them less than men.

An audit of JPMorgan’s Investment Bank, Technology and Market Strategies functional unit revealed a statistical compensation disparity between men and women in lead application developer, project manager, and technology director positions since at least May 2012, the DOL’s Office of Federal Contract Compliance Programs alleged in a January administrative complaint. The disparity remained even after accounting for “legitimate compensation-determining factors,” the agency said.

JPMorgan sought dismissal of the claims, but an administrative law...