An appellate court issued an emergency order on Monday that will allow Drake’s Bay Oyster Company to continue doing business while the embattled cannery wages a legal battle against the Obama administration.

A three-judge panel of the U.S. Court of Appeals for the Ninth Circuit granted oysterman Kevin Lunny’s eleventh-hour request “because there are serious legal questions and the balance of hardships tips sharply in [Mr. Lunny’s] favor.”

The ruling allows the cannery’s offshore operations to continue in Point Reyes National Seashore despite a decision three months ago by Interior Secretary Ken Salazar to let the lease expire. A lower court judge ruled earlier this month that an injunction was unwarranted because courts lacked jurisdiction over Mr. Salazar’s decision and because Mr. Lunny was unlikely to succeed in court. That ruling will be  reconsidered by the Ninth Circuit in May.

Mr. Lunny’s lawyers have argued in court their business will fail without an injunction order pending the outcome of their lawsuit against Mr. Salazar and the National Park Service. The National Park Service had ordered Mr. Lunny to unwind his offshore operations by Thursday.

“We are beyond thrilled that our business will now remain open while we continue to fight the decisions from the court and Secretary Salazar that have put our business at risk,” Mr. Lunny said in a statement. “We are so grateful for the support we continue to receive from the community and our legal team and we now will press on in our fight as the lawsuit proceeds. Our fight has always been about more than just our business. Our fight is, and will continue to be, about the great service Drakes Bay Oyster Farm provides to the community as an innovative sustainable farm, an educational resource, and part of the economic fiber of Marin County.”

The debate that raged over Drake’s Bay’s lease vexed scientists and environmental activists on opposite ends of the issue. Some local and national groups argued that oyster farming was deleterious to the environment and asked that the estuary be restored to wilderness. Others said the business was a boon to the local economy, the farm’s 31 employees and shellfish consumers.