In theory, terrorists could use select agents as weapons, so the government requires any organization that wants to handle them to pass a background check, register, follow safety and security procedures, and undergo inspections through a program run by the C.D.C. and the United States Department of Agriculture. As of 2017, 263 laboratories — government, academic, commercial or private — had registered with the program.

The institute at Fort Detrick was part of the select agent program until its registration was suspended last month, after the C.D.C. ordered it to stop conducting the research.

The shutdown was first reported on Friday by the Frederick News-Post.

The problems date back to May 2018, when storms flooded and ruined a decades-old steam sterilization plant that the institute had been using to treat wastewater from its labs, Ms. Vander Linden said. The damage halted research for months, until the institute developed a new decontamination system using chemicals.

The new system required changes in certain procedures in the laboratories. During an inspection in June, the C.D.C. found that the new procedures were not being followed consistently. Inspectors also found mechanical problems with the chemical-based decontamination system, as well as leaks, Ms. Vander Linden said, though she added that the leaks were within the lab and not to the outside world.

“A combination of things” led to the cease and desist order, and the loss of registration, she said.

Dr. Richard H. Ebright, a molecular biologist and bioweapons expert at Rutgers University, said in an email that problems with the institute’s new chemical-based decontamination process might mean it would have to go back to a heat-based system “which, if it requires constructing a new steam sterilization plant, could entail very long delays and very high costs.”

Although many projects are on hold, Ms. Vander Linden said scientists and other employees are continuing to work, just not on select agents. She said many were worried about not being able meet deadlines for their projects.