SAN FRANCISCO — Much of Chief Judge Vaughn Walker’s latest message for the Justice Department in a closely watched warrantless wiretap case is simple: Maybe you had a secret warrant, but since you won’t produce it, deal with the consequences.

In a summary judgment grant to Al-Haramain Islamic Foundation Inc. on Wednesday, Walker found that the government eavesdropped on the Oregon nonprofit without obtaining a warrant from a special national security court. That violated congressional guidelines on how to legally conduct domestic surveillance, Walker wrote.