In the same order, U.S. District Judge Royce Lamberth denied a request by Defense Secretary Donald Rumsfeld and other senior military officials to disclose the identities of the Doe plaintiffs.
The Army has implemented a "stop loss" policy that prevents tens of thousands of soldiers designated to serve in Iraq and Afghanistan from leaving the military when their volunteer service commitment is over. Critics contend the policy amounts to a backdoor draft, a claim the military has strongly rejected.
The three John Does are among seven soldiers who joined in a federal lawsuit in January to fight the policy. All were serving in Iraq or headed to Iraq from Kuwait.
The lead plaintiff, Spec. David Qualls, was the only one named in the suit. The others, each described as John Doe, asked to remain anonymous because they feared retaliation.
"Fears of embarrassment or vague, unsubstantiated fears of retaliatory action by higher-ups do not permit a plaintiff to proceed under a pseudonym," Lamberth wrote.
"None of the evidence demonstrates that Doe plaintiffs are likely to face physical retaliation as a result of filing this lawsuit," the ruling said.
"The court will not permit Doe plaintiffs to proceed under pseudonyms. However, the court will not give the defendants the specific relief they request - the unsealing of the Doe plaintiffs' filing that contains real names and addresses," Lamberth said in a ten-page ruling.
Lamberth dismissed the claims of three of the John Does who declined to submit their real names to the court under seal. He ordered the others to submit their names within five days or have their claims against the military thrown out.