The newspaper and Ward argued that death certificates are public records, while the health department said state law requires it to restrict access to the information.
Senior Vanderburgh Circuit Court Judge Carl Heldt ruled Monday in the county's favor.
The Courier & Press had published causes of death on its Sunday public records page from 2002 until May 2012, when the health department abruptly stopped including that information. Courier & Press Editor Tim Ethridge said the newspaper is weighing whether it will appeal the ruling.
Indiana's public access counselor, Joseph Hoage, wrote in a July opinion that a state law that took effect in January 2011 says that showing one has a direct interest to get cause of death information is only applicable to the state's death registration system.
He wrote that another Indiana law still required local health departments to keep records of the death certificates filed by physicians and make them available to the public.
The county contends the 2011 law restricts cause of death information only to those who can prove they have a direct interest in it, such as a spouse or immediate relative who may need it for legal purposes.
Heldt acknowledged in his ruling that the two laws conflicted but said that in cases when conflicting laws can't be reconciled, the more specific law should apply. He said the law cited by the county is more specific.
Indiana's 2011 law created an electronic Indiana Death Registration System, which Vanderburgh County Health Department Administrator Gary Heck said eliminated all paper copies of death records and is maintained solely by the state.
County attorney Joseph Harrison Jr. said that all of the death certificates are now maintained through the state's electronic system.
"Those can be run out and given to those they determine meet the criteria in the state law but they don't keep a copy in the files like they used to do," he said.
Heldt wrote in his decision that the court could not order the county to produce records it does not possess.
But attorney Pat Shoulders, who represented the newspaper, said that incident seemed to show that the county did in fact have the records.
"I'm especially troubled by that part of the court's ruling which seems to suggest that the county can't produce records they don't have. They indeed have these records," Shoulders said.