The Obama administration last week asked an appeals court to uphold an order closing Drake’s Bay Oyster Company (DBOC) as the embattled cannery’s Republican allies pressed federal officials to release more documents explaining their decision to restore the company’s accommodations to wilderness.

The Department of the Interior has been silent publicly since outgoing Secretary Ken Salazar denied oysterman Kevin Lunny’s request for a new permit in November pending the outcome of a lawsuit that has allowed Mr. Lunny to overstay his tenancy for now. The government’s written rebuttal on Wednesday allowed the government another opportunity to rehearse its arguments for judges in advance of a hearing before an appeals court next month that could be decisive.

Two days after the government’s arguments were filed with the United States Court of Appeals for the Ninth Circuit, the chairman of the House of Representatives’ Committee on Natural Resources sent letters to Mr. Salazar and the agency’s official watchdog, Mary Kendall, asking for reams of documents to show how Mr. Salazar arrived at his decision to deny the permit and how Ms. Kendall’s Office of the Inspector General came to dismiss scientific integrity complaints made by an advocate for Mr. Lunny.

The request for documents came from Doc Hastings, a Washington State Republican, one of several Congressional Republicans who has joined Mr. Lunny’s strange-bedfellows coalition of supporters. Representative Hastings has also previously accused Ms. Kendall of deferential treatment to the agency officials she audits. “It is imperative that the Department’s decision be based in sound science and consistent with federal law,” the letter to Mr. Salazar read. In a statement, Representative Hastings’ office said serious questions were “raised about the science used by the National Park Service to justify the closure of the farm.”

Representative Hastings requested that Mr. Salazar’s notes and drafts of his decision, every email between senior Interior Department officials and environmental groups like the National Parks Conservation Association and supporting documentation used in Ms. Kendall’s audit be provided by April 26.

The committee’s investigation is unlikely to impact Mr. Lunny’s current appeal to stay open, according to Ryan Waterman, a member of the oyster farm’s legal team, but the facts could become evidence later in the ongoing lawsuit against the federal government, as Mr. Lunny’s case for survival relies on questions of intent—not his, but the federal government’s.

One key question in the lawsuit is whether a small section of a 2009 bill drafted by Dianne Feinstein gave Mr. Salazar unassailable authority to deny the oyster company a new permit. “Congress did not put a thumb on the scale in DBOC’s favor,” the government argued. “Rather, it balanced the scale, allowing the Secretary to weigh the factors he deemed relevant and choose among several possible outcomes.”

Mr. Lunny’s lawyers said that federal law imposed conditions on Mr. Salazar’s discretion that he failed to meet by considering “defective data and junk science.” Government lawyers argue that the park service should not be penalized for doing more than the law requires” in issuing a disputed environmental impact statement.

Representative Hastings’ letter did give credence to the government’s claim that Mr. Salazar’s discretion was not limited by any laws, a fact that was seized upon by Drake’s Bay opponent Amy Trainer, who leads the Environmental Action Committee of West Marin.

“It appears that the corporation’s deep-dive into special interest, right-wing politics has backfired, as the company’s conduits can’t keep their story straight in the rabid attempt to attack national parks, and are in fact making statements that inadvertently undermine the corporation’s own arguments before the court,” Ms. Trainer said in a statement. “Apparently right-wing politicians and industry lobbyists on Capitol Hill have made this policy-based decision about protecting our most special waters into a national cause celebre of conservatives.”

The oyster farm continues to operate because of an emergency ruling by a panel of the appeals court that temporarily overrode a lower-court ruling. Government lawyers say the appellate court should now agree with the ruling that Mr. Lunny says would put him of business—regardless of the outcome of the lawsuit—by forcing him to vacate federal land and destroy at least 19 million shellfish, worth an estimated $9.5 million, growing in the estuary.

The government argued that Mr. Lunny knew that his right to use Drakes Estero was going to expire in 2012, and the district court judge found that Mr. Lunny’s lack of foresight—or “unfounded hopes”—weighed against his claim that the denial of the permit will cause some hardship for his employees and the community. Government lawyers wrote that Mr. Lunny and the previous owner of the oyster farm “have enjoyed the full benefits of their bargains.”

Mr. Lunny’s legal team will respond to the government’s arguments by April 22, three weeks before the oral argument. “What we see in the Department of the Interior’s latest response brief are the same flawed arguments that they brought to the U.S. District Court,” said Mary Beth Hutchins, a spokeswoman for Cause of Action, a watchdog organization contributing to Mr. Lunny’s legal case.