WASHINGTON — Chief Justice John G. Roberts Jr. did not seem happy during a Supreme Court argument Monday about whether the Clean Water Act applies to runoff from logging roads. The source of his frustration was a last-minute action from the Environmental Protection Agency that was calculated to address the legal issues before the court.

‘‘Were you as surprised as we were?’’ Roberts asked a lawyer for the government, referring to a new regulation, issued Friday afternoon, that said permits are not required for the runoff at issue in the case.