A naval officer has received an honorable discharge after filing a writ of habeas corpus in November claiming the Navy had refused to release him as a conscientious objector.

The officer, Michael Izbicki, submitted two applications for conscientious objector status, saying military service of any kind conflicted with his beliefs as a Quaker. The U.S. Navy denied both requests.

But in November, the American Civil Liberties Union of Connecticut filed a writ of habeas corpus in federal court on his behalf. The Navy has since reconsidered his request, granting him an honorable discharge with the understanding that the service will recoup the pro-rated costs of his advanced education, according to a Tuesday ACLU statement.

“It should not have taken the filing of a federal lawsuit for the Navy to recognize Michael Izbicki as a sincere conscientious objector, consistent with law and its own regulations.  All of the facts in the lawsuit were presented to the Navy by Michael Izbicki before the filing of the lawsuit,” Deborah H. Karpatkin, a cooperating attorney from New York on the case said. “The Navy has finally looked properly at the entire record in this case and now correctly recognized that Michael Izbicki is a sincere conscientious objector based on his religious beliefs against participation in war in any form.”

Izbicki, who had been an ensign assigned to a submarine base in Groton, said he was glad to be free of the constant conflict he faced between his job and religious principles.

“I’m relieved the Navy recognized that my religious beliefs made it impossible for me to serve in the Navy,” he said in a prepared statement. “I look forward to serving my country in some peaceful capacity.”