The U.S. government spent $34 million to help an Alpharetta-based pharmaceutical company test a treatment to battle flu pandemics, but it halted its backing because of “significant challenges” that could cause delays and cost increases, according to a federal official.

Now, the government is trying to decide whether to continue its contract with Biota Pharmaceuticals or try another option, according to Robin Robinson, the director of the Biomedical Advanced Research and Development Authority (BARDA), which is part of the U.S. Department of Health and Human Services.

“The progress of the development has been slower than anticipated,” Robinson wrote in an email Wednesday to The Atlanta Journal-Constitution.

It is uncommon for BARDA to stop work on a project.

The authority is building a system to develop and buy medicines and other material for public health emergencies. BARDA supports more than 50 medicines, diagnostics and vaccines tied to influenza.

Robinson’s comments come a day after Biota disclosed that the government had issued a stop-work order on its contract. At the time, the company said it was surprised and didn’t have any additional understanding of the pending decision. The news sent Biota’s stock price plummeting.

Biota Chief Executive Russell Plumb did not respond to AJC requests for comment.

The U.S. government had agreed in 2011 to spend up to $231.2 million over five years on the development of Biota’s flu treatment, laninamivir octanoate. The money was to be spent on further developing the drug, including running clinical trials toward getting federal drug approval and providing U.S.-based manufacturing.

The product has already been approved for use in Japan, where it is on the market.

Robinson said BARDA does not have safety concerns about the drug. But concerns had arisen about the enrollment of subjects in clinical trials, the cost of additional trials, the “emergence of resistance to laninamivir in recent H7N9 virus strains, and the feasibility of laninamivir for treatment of critically ill, hospitalized patients with influenza.”

The government “issued a stop-work order to deliberate on the best course of action going forward for this project and the BARDA influenza antiviral drug program.”

Robinson wrote that he couldn’t provide a date for when a decision would be made on the project.

Biota moved its headquarters to Alpharetta from Maryland last year. Much of the company’s focus recently had been around its flu treatment.