OAKLAND — A federal judge Friday heard arguments but delayed a decision on a bid by Drakes Bay Oyster Co. to avert a government-ordered shutdown while the company’s legal challenge is resolved.

U.S. District Judge Yvonne Gonzalez Rogers conducted the hearing before a packed courtroom while a crowd of more than 50 people was left standing in front of the federal courthouse in downtown Oakland.

Kevin Lunny, operator of the embattled oyster farm in the 2,500-acre Drakes Estero in Point Reyes National Seashore, is fighting Interior Secretary Ken Salazar’s decision Nov. 29 denying renewal of the operation’s federal permit.

The judge did not indicate when she would rule on the request for an injunction but seemed to cast doubt on the oyster company’s case when she questioned whether the court has jurisdiction in the matter.

“Now, it’s waiting time,” Lunny said in the federal building courtyard after the hearing.

Drakes Bay Oyster Co. plants and harvests 8 million oysters — worth about $1.5 million a year — from the estero, a five-fingered estuary in the national seashore in Marin County.

The judge did not say when she would issue a decision, said Lunny and his attorney, Amber Abbasi, of the Washington, D.C.-based nonprofit group Cause of Action.

Lunny, who was born and raised on a ranch next to the estero, said he was “absolutely hopeful” of a favorable decision. “This is a matter of law. Our attorneys did a beautiful job.”

Sen. Dianne Feinstein’s legislation in 2009 gave Salazar sole discretion to renew the oyster farm’s permit, issued 40 years ago to a previous owner of the oyster farm, which Lunny acquired in 2004.

Four days after Salazar’s decision, Lunny filed the lawsuit alleging it violated federal environmental rules and was based on faulty science.

But without a stay of the Feb. 28 deadline to shut down, Lunny said his enterprise, which employs 31 full-time workers, will be lost.

If he is forced to lay off the staff, remove their housing and kill 19 million oysters in the estero, “there’s no recovering this business,” he said.

Lunny said he is already scaling back the operation, harvesting oysters but no longer planting oyster larvae in the estero’s clear, cold water.

“It’s hard to look at what could happen here,” Lunny said. “It could devastate a small community.”

The prolonged battle over Drakes Bay Oyster Co. pits supporters of West Marin County agriculture, who fear that Salazar’s decision foretells the loss of permits for onshore ranches in the national seashore, versus wilderness advocates who insist that all human activity must be removed from the estero based on its congressional designation as a wilderness area.

Abbasi said she thought the judge “seemed very interested in the irreparable harm,” referring to Lunny’s claim that an ultimate victory in court would do no good if he has to shut down in a matter of weeks.

Abbasi said Judge Rogers’ decision on Lunny’s request to stay in business could be appealed.

Lawyers for Salazar said in court papers that his decision was not subject to environmental rules and that the “allegations of scientific misconduct are baseless.”

Salazar’s decision was “based on the incompatibility of commercial activities in wilderness and not on … data that was asserted to be flawed.”

Lunny’s loss of business was “a foreseeable consequence” of buying the oyster farm in 2004.

Lunny noted Friday that oysters have been harvested from Drakes Estero since 1934.